I hope that should read: “I’m on live ISO and in cachy-chroot”, because otherwise you would just update your live environment, which is not your goal.
Thanks for linking it, I’ll read it more carefully next time I run into a pacnew. I’ve seen that post a few days ago but lost it.
You are correct, it was cachy-chroot, I was following a guide and I checked that the user is [root@CachyOS /]#.
Well, my update was failing even last week, before I’ve accepted the pacnew. I thought that must fix it but it did indeed make things worse.
Anyway, I’ve run the update on cachy-chroot and I still ended up in emergency mode. So I’ve rolled back, fixed the pacman.conf and will try again later today with
pacman -Qqn | sudo pacman -S -
Fingers crossed.
This reinstalls all packages, it’s a pretty drastic Hail Mary measure. Are you sure this is what you want to do?
If you roll back to before the problem began, updating should just work. And, if it doesn’t, there’s probably a reason, and it’s unlikely force reinstalling everything will fix it.
Your “Konsole” link in OP 404s.
What exactly are you trying to fix / what does sudo pacman -Syu output after you rollback and/or fix the pacman.conf?
That link had not much different from this post I’ve made after that, only it was the full log with all the different package warnings.
I’m opting for that command because that’s in this guide on migrating to a new architecture. Turns out I’ve somehow managed tu un-Cachy my system so it does probably make sense to make sure all the packages are perfectly synced.
I mean, I can try to run just a regular sudo pacman -Syu first and see what happens. What’s one more rollback among friends, right?
Welp, I ran sudo pacman -Syu and ended up on the emergency screen again.
This is how my pacman.conf is now, this should be fine now, right?
#
# /etc/pacman.conf
#
# See the pacman.conf(5) manpage for option and repository directives
#
# GENERAL OPTIONS
#
[options]
# The following paths are commented out with their default values listed.
# If you wish to use different paths, uncomment and update the paths.
#RootDir = /
#DBPath = /var/lib/pacman/
#CacheDir = /var/cache/pacman/pkg/
#LogFile = /var/log/pacman.log
#GPGDir = /etc/pacman.d/gnupg/
#HookDir = /etc/pacman.d/hooks/
HoldPkg = pacman glibc
#XferCommand = /usr/bin/curl -L -C - -f -o %o %u
#XferCommand = /usr/bin/wget --passive-ftp -c -O %o %u
#CleanMethod = KeepInstalled
Architecture = auto
# Pacman won't upgrade packages listed in IgnorePkg and members of IgnoreGroup
#IgnorePkg =
#IgnoreGroup =
#NoUpgrade =
#NoExtract =
# Misc options
#UseSyslog
#Color
#NoProgressBar
#PrettyProgressBar
#ILoveCandy
CheckSpace
#VerbosePkgLists
ParallelDownloads = 5
DownloadUser = alpm
#DisableSandbox
#DisableSandboxFilesystem
#DisableSandboxSyscalls
# By default, pacman accepts packages signed by keys that its local keyring
# trusts (see pacman-key and its man page), as well as unsigned packages.
SigLevel = Required DatabaseOptional
LocalFileSigLevel = Optional
#RemoteFileSigLevel = Required
# NOTE: You must run `pacman-key --init` before first using pacman; the local
# keyring can then be populated with the keys of all official Arch Linux
# packagers with `pacman-key --populate archlinux`.
#
# REPOSITORIES
# - can be defined here or included from another file
# - pacman will search repositories in the order defined here
# - local/custom mirrors can be added here or in separate files
# - repositories listed first will take precedence when packages
# have identical names, regardless of version number
# - URLs will have $repo replaced by the name of the current repo
# - URLs will have $arch replaced by the name of the architecture
#
# Repository entries are of the format:
# [repo-name]
# Server = ServerName
# Include = IncludePath
#
# The header [repo-name] is crucial - it must be present and
# uncommented to enable the repo.
#
# The testing repositories are disabled by default. To enable, uncomment the
# repo name header and Include lines. You can add preferred servers immediately
# after the header, and they will be used before the default mirrors.
#[core-testing]
#Include = /etc/pacman.d/mirrorlist
#[extra-testing]
#Include = /etc/pacman.d/mirrorlist
[cachyos-znver4]
Include = /etc/pacman.d/cachyos-v4-mirrorlist
[cachyos-core-znver4]
Include = /etc/pacman.d/cachyos-v4-mirrorlist
[cachyos-extra-znver4]
Include = /etc/pacman.d/cachyos-v4-mirrorlist
[cachyos]
Include = /etc/pacman.d/cachyos-mirrorlist
[core]
Include = /etc/pacman.d/mirrorlist
[extra]
Include = /etc/pacman.d/mirrorlist
# If you want to run 32 bit applications on your x86_64 system,
# enable the multilib repositories as required here.
#[multilib-testing]
#Include = /etc/pacman.d/mirrorlist
[multilib]
Include = /etc/pacman.d/mirrorlist
# An example of a custom package repository. See the pacman manpage for
# tips on creating your own repositories.
#[custom]
#SigLevel = Optional TrustAll
#Server = file:///home/custompkgs
I haven’t noticed anything suspicious as the upgrade was running. Can I fetch you something from cachy-chroot?
Is it time for pacman -Qqn | sudo pacman -S - or is there a better option before that?
I’m looking through the forum to see what people have pulled for diagnosing their emergency screen issues.
So, here’s pacman.log. I’ve kept only the beginning, the colorful lines amidst the upgrading and the end;
[2026-02-27T20:24:18+0100] [PACMAN] Running ‘pacman -Syu’
[2026-02-27T20:24:18+0100] [PACMAN] synchronizing package lists
[2026-02-27T20:24:37+0100] [PACMAN] starting full system upgrade
[2026-02-27T20:42:20+0100] [ALPM] running ‘05-snap-pac-pre.hook’…
[2026-02-27T20:42:21+0100] [ALPM-SCRIPTLET] ==> root: 124
[2026-02-27T20:42:21+0100] [ALPM] running ‘10-limine-snapper-lock.hook’…
[2026-02-27T20:42:23+0100] [ALPM] running ‘60-limine-mkinitcpio-remove-pre.hook’…
[2026-02-27T20:42:24+0100] [ALPM] running ‘60-mkinitcpio-remove.hook’…
[2026-02-27T20:42:24+0100] [ALPM] running ‘71-dkms-remove.hook’…
[2026-02-27T20:42:24+0100] [ALPM-SCRIPTLET] ==> dkms remove --no-depmod hid-xpadneo/v0.9.8 -k 6.19.0-2-cachyos
[2026-02-27T20:42:24+0100] [ALPM-SCRIPTLET] ==> dkms remove --no-depmod hid-xpadneo/v0.9.8 -k 6.18.10-2-cachyos-lts
[2026-02-27T20:42:25+0100] [ALPM-SCRIPTLET] ==> depmod 6.19.0-2-cachyos
[2026-02-27T20:42:26+0100] [ALPM-SCRIPTLET] ==> depmod 6.18.10-2-cachyos-lts
[2026-02-27T20:42:28+0100] [ALPM] transaction started
[2026-02-27T20:42:28+0100] [ALPM] upgraded iana-etc (20260203-1 → 20260225-2)
[2026-02-27T20:42:28+0100] [ALPM] upgraded glibc (2.43+r5+g856c426a7534-2 → 2.43+r5+g856c426a7534-3)
[2026-02-27T20:42:28+0100] [ALPM-SCRIPTLET] Generating locales…
[2026-02-27T20:42:29+0100] [ALPM-SCRIPTLET] cs_CZ.UTF-8… done
[2026-02-27T20:42:29+0100] [ALPM-SCRIPTLET] en_US.UTF-8… done
[2026-02-27T20:42:29+0100] [ALPM-SCRIPTLET] Generation complete.
[2026-02-27T20:42:30+0100] [ALPM] upgraded libgpg-error (1.58-1.1 → 1.59-1.1)
[2026-02-27T20:42:31+0100] [ALPM] warning: directory permissions differ on /boot/, filesystem: 700 package: 755
[2026-02-27T20:42:31+0100] [ALPM] upgraded shared-mime-info (2.4-2.1 → 2.4-3.1)
[2026-02-27T20:42:36+0100] [ALPM] warning: /etc/pacman.d/mirrorlist installed as /etc/pacman.d/mirrorlist.pacnew
[2026-02-27T20:42:40+0100] [ALPM] upgraded lib32-libgpg-error (1.58-1 → 1.59-1)
[2026-02-27T20:42:42+0100] [ALPM] warning: /etc/limine-snapper-sync.conf installed as /etc/limine-snapper-sync.conf.pacnew
[2026-02-27T20:42:52+0100] [ALPM] upgraded python-pillow (12.1.0-2 → 12.1.1-1)
[2026-02-27T20:42:52+0100] [ALPM] upgraded sd (1.0.0-1.1 → 1.1.0-1.1)
[2026-02-27T20:42:52+0100] [ALPM] upgraded spdlog (1.17.0-1.1 → 1.17.0-2.1)
[2026-02-27T20:42:52+0100] [ALPM] installed kquickimageeditor (0.6.0-2.1)
[2026-02-27T20:42:52+0100] [ALPM] upgraded spectacle (1:6.5.5-1.1 → 1:6.6.1-1.1)
[2026-02-27T20:42:52+0100] [ALPM] upgraded systemd-resolvconf (259.1-1 → 259.2-1)
[2026-02-27T20:42:52+0100] [ALPM] upgraded systemd-sysvcompat (259.1-1 → 259.2-1)
[2026-02-27T20:42:52+0100] [ALPM] upgraded tealdeer (1.8.1-1.1 → 1.8.1-2.1)
[2026-02-27T20:42:53+0100] [ALPM] upgraded vim-runtime (9.1.2132-1.1 → 9.2.0067-1.1)
[2026-02-27T20:42:53+0100] [ALPM] upgraded vim (9.1.2132-1.1 → 9.2.0067-1.1)
[2026-02-27T20:42:53+0100] [ALPM] upgraded wireless-regdb (2025.10.07-1 → 2026.02.04-1)
[2026-02-27T20:42:53+0100] [ALPM] upgraded xl2tpd (1.3.19-1.1 → 1.3.20-1.1)
[2026-02-27T20:42:53+0100] [ALPM] transaction completed
[2026-02-27T20:42:55+0100] [ALPM] running ‘20-systemd-sysusers.hook’…
[2026-02-27T20:42:55+0100] [ALPM] running ‘21-systemd-tmpfiles.hook’…
[2026-02-27T20:42:55+0100] [ALPM-SCRIPTLET] /usr/lib/tmpfiles.d/systemd.conf:35: Duplicate line for path “/var/lib/systemd/coredump”, ignoring.
[2026-02-27T20:42:55+0100] [ALPM] running ‘25-systemd-catalog.hook’…
[2026-02-27T20:42:55+0100] [ALPM] running ‘25-systemd-hwdb.hook’…
[2026-02-27T20:42:56+0100] [ALPM] running ‘25-systemd-sysctl.hook’…
[2026-02-27T20:42:56+0100] [ALPM] running ‘30-systemd-daemon-reload-system.hook’…
[2026-02-27T20:42:56+0100] [ALPM] running ‘30-systemd-daemon-reload-user.hook’…
[2026-02-27T20:42:56+0100] [ALPM] running ‘30-update-mime-database.hook’…
[2026-02-27T20:42:57+0100] [ALPM] running ‘35-systemd-restart-marked.hook’…
[2026-02-27T20:42:57+0100] [ALPM] running ‘35-systemd-udev-reload.hook’…
[2026-02-27T20:43:00+0100] [ALPM] running ‘35-systemd-update.hook’…
[2026-02-27T20:43:01+0100] [ALPM] running ‘40-update-ca-trust.hook’…
[2026-02-27T20:43:01+0100] [ALPM] running ‘60-depmod.hook’…
[2026-02-27T20:43:03+0100] [ALPM] running ‘70-dkms-install.hook’…
[2026-02-27T20:43:03+0100] [ALPM-SCRIPTLET] ==> dkms install --no-depmod hid-xpadneo/v0.9.8 -k 6.18.14-2-cachyos-lts
[2026-02-27T20:43:04+0100] [ALPM-SCRIPTLET] ==> dkms install --no-depmod hid-xpadneo/v0.9.8 -k 6.19.4-2-cachyos
[2026-02-27T20:43:06+0100] [ALPM-SCRIPTLET] ==> depmod 6.18.14-2-cachyos-lts
[2026-02-27T20:43:07+0100] [ALPM-SCRIPTLET] ==> depmod 6.19.4-2-cachyos
[2026-02-27T20:43:09+0100] [ALPM] running ‘80-limine-efi-deploy.hook’…
[2026-02-27T20:43:09+0100] [ALPM-SCRIPTLET] Limine EFI install completed successfully.
[2026-02-27T20:43:09+0100] [ALPM] running ‘90-limine-mkinitcpio-remove-post.hook’…
[2026-02-27T20:43:09+0100] [ALPM] running ‘90-mkinitcpio-install.hook’…
[2026-02-27T20:43:10+0100] [ALPM-SCRIPTLET] Building initramfs for linux-cachyos-lts (6.18.14-2-cachyos-lts)
[2026-02-27T20:43:10+0100] [ALPM-SCRIPTLET] ==> Using drop-in configuration file: ‘10-chwd.conf’
[2026-02-27T20:43:10+0100] [ALPM-SCRIPTLET] ==> Using drop-in configuration file: ‘10-limine-snapper-sync.conf’
[2026-02-27T20:43:10+0100] [ALPM-SCRIPTLET] ==> Starting build: ‘6.18.14-2-cachyos-lts’
[2026-02-27T20:43:10+0100] [ALPM-SCRIPTLET] → Running build hook: [base]
[2026-02-27T20:43:10+0100] [ALPM-SCRIPTLET] → Running build hook: [systemd]
[2026-02-27T20:43:10+0100] [ALPM-SCRIPTLET] → Running build hook: [autodetect]
[2026-02-27T20:43:11+0100] [ALPM-SCRIPTLET] → Running build hook: [microcode]
[2026-02-27T20:43:11+0100] [ALPM-SCRIPTLET] → Running build hook: [kms]
[2026-02-27T20:43:13+0100] [ALPM-SCRIPTLET] → Running build hook: [modconf]
[2026-02-27T20:43:13+0100] [ALPM-SCRIPTLET] → Running build hook: [block]
[2026-02-27T20:43:14+0100] [ALPM-SCRIPTLET] → Running build hook: [keyboard]
[2026-02-27T20:43:14+0100] [ALPM-SCRIPTLET] → Running build hook: [sd-vconsole]
[2026-02-27T20:43:14+0100] [ALPM-SCRIPTLET] → Running build hook: [plymouth]
[2026-02-27T20:43:15+0100] [ALPM-SCRIPTLET] → Running build hook: [filesystems]
[2026-02-27T20:43:15+0100] [ALPM-SCRIPTLET] → Running build hook: [sd-btrfs-overlayfs]
[2026-02-27T20:43:15+0100] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2026-02-27T20:43:15+0100] [ALPM-SCRIPTLET] ==> Creating zstd-compressed initcpio image: ‘/tmp/staging_initramfs.img’
[2026-02-27T20:43:15+0100] [ALPM-SCRIPTLET] → Early uncompressed CPIO image generation successful
[2026-02-27T20:43:16+0100] [ALPM-SCRIPTLET] ==> Initcpio image generation successful
[2026-02-27T20:43:16+0100] [ALPM-SCRIPTLET] Kernel stored in /boot/661936192dc5404bb52d007a0084368a/linux-cachyos-lts/vmlinuz-linux-cachyos-lts
[2026-02-27T20:43:16+0100] [ALPM-SCRIPTLET] Initramfs stored in /boot/661936192dc5404bb52d007a0084368a/linux-cachyos-lts/initramfs-linux-cachyos-lts
[2026-02-27T20:43:16+0100] [ALPM-SCRIPTLET] e[1;32mUpdated:e[0m /boot/limine.conf
[2026-02-27T20:43:16+0100] [ALPM-SCRIPTLET] Building initramfs for linux-cachyos (6.19.4-2-cachyos)
[2026-02-27T20:43:16+0100] [ALPM-SCRIPTLET] ==> Using drop-in configuration file: ‘10-chwd.conf’
[2026-02-27T20:43:16+0100] [ALPM-SCRIPTLET] ==> Using drop-in configuration file: ‘10-limine-snapper-sync.conf’
[2026-02-27T20:43:16+0100] [ALPM-SCRIPTLET] ==> Starting build: ‘6.19.4-2-cachyos’
[2026-02-27T20:43:16+0100] [ALPM-SCRIPTLET] → Running build hook: [base]
[2026-02-27T20:43:16+0100] [ALPM-SCRIPTLET] → Running build hook: [systemd]
[2026-02-27T20:43:17+0100] [ALPM-SCRIPTLET] → Running build hook: [autodetect]
[2026-02-27T20:43:17+0100] [ALPM-SCRIPTLET] → Running build hook: [microcode]
[2026-02-27T20:43:17+0100] [ALPM-SCRIPTLET] → Running build hook: [kms]
[2026-02-27T20:43:20+0100] [ALPM-SCRIPTLET] → Running build hook: [modconf]
[2026-02-27T20:43:20+0100] [ALPM-SCRIPTLET] → Running build hook: [block]
[2026-02-27T20:43:21+0100] [ALPM-SCRIPTLET] → Running build hook: [keyboard]
[2026-02-27T20:43:21+0100] [ALPM-SCRIPTLET] → Running build hook: [sd-vconsole]
[2026-02-27T20:43:21+0100] [ALPM-SCRIPTLET] → Running build hook: [plymouth]
[2026-02-27T20:43:22+0100] [ALPM-SCRIPTLET] → Running build hook: [filesystems]
[2026-02-27T20:43:22+0100] [ALPM-SCRIPTLET] → Running build hook: [sd-btrfs-overlayfs]
[2026-02-27T20:43:22+0100] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2026-02-27T20:43:22+0100] [ALPM-SCRIPTLET] ==> Creating zstd-compressed initcpio image: ‘/tmp/staging_initramfs.img’
[2026-02-27T20:43:22+0100] [ALPM-SCRIPTLET] → Early uncompressed CPIO image generation successful
[2026-02-27T20:43:22+0100] [ALPM-SCRIPTLET] ==> Initcpio image generation successful
[2026-02-27T20:43:22+0100] [ALPM-SCRIPTLET] Kernel stored in /boot/661936192dc5404bb52d007a0084368a/linux-cachyos/vmlinuz-linux-cachyos
[2026-02-27T20:43:23+0100] [ALPM-SCRIPTLET] Initramfs stored in /boot/661936192dc5404bb52d007a0084368a/linux-cachyos/initramfs-linux-cachyos
[2026-02-27T20:43:23+0100] [ALPM-SCRIPTLET] e[1;32mUpdated:e[0m /boot/limine.conf
[2026-02-27T20:43:23+0100] [ALPM] running ‘accounts-daemon-restart.hook’…
[2026-02-27T20:43:23+0100] [ALPM] running ‘cachyos-reboot-required.hook’…
[2026-02-27T20:43:23+0100] [ALPM-SCRIPTLET] ==> INFO: Reboot is recommended due to the upgrade of core system package(s).
[2026-02-27T20:43:23+0100] [ALPM] running ‘dbus-reload.hook’…
[2026-02-27T20:43:23+0100] [ALPM] running ‘detect-old-perl-modules.hook’…
[2026-02-27T20:43:23+0100] [ALPM] running ‘fontconfig.hook’…
[2026-02-27T20:43:23+0100] [ALPM] running ‘fontconfig-32.hook’…
[2026-02-27T20:43:24+0100] [ALPM] running ‘gtk-update-icon-cache.hook’…
[2026-02-27T20:43:24+0100] [ALPM] running ‘rebuild-detector.hook’…
[2026-02-27T20:43:31+0100] [ALPM] running ‘texinfo-install.hook’…
[2026-02-27T20:43:32+0100] [ALPM] running ‘update-desktop-database.hook’…
[2026-02-27T20:43:32+0100] [ALPM] running ‘vimdoc.hook’…
[2026-02-27T20:43:32+0100] [ALPM] running ‘zz-snap-pac-post.hook’…
[2026-02-27T20:43:33+0100] [ALPM-SCRIPTLET] ==> root: 125
Here’s fstab;
/etc/fstab: static file system information.
Use ‘blkid’ to print the universally unique identifier for a device; this may
be used with UUID= as a more robust way to name devices that works even if
disks are added and removed. See fstab(5).
UUID=41E2-ABC8 /boot vfat defaults,umask=0077 0 2
UUID=cd90e23e-44ba-4626-9af0-f0b55875e4a7 / btrfs subvol=/@,defaults,noatime,compress=zstd:1 0 0
UUID=cd90e23e-44ba-4626-9af0-f0b55875e4a7 /home btrfs subvol=/@home,defaults,noatime,compress=zstd:1 0 0
UUID=cd90e23e-44ba-4626-9af0-f0b55875e4a7 /root btrfs subvol=/
,defaults,noatime,compress=zstd:1 0 0
UUID=cd90e23e-44ba-4626-9af0-f0b55875e4a7 /srv btrfs subvol=/@srv,defaults,noatime,compress=zstd:1 0 0
UUID=cd90e23e-44ba-4626-9af0-f0b55875e4a7 /var/cache btrfs subvol=/@cache,defaults,noatime,compress=zstd:1 0 0
UUID=cd90e23e-44ba-4626-9af0-f0b55875e4a7 /var/tmp btrfs subvol=/@tmp,defaults,noatime,compress=zstd:1 0 0
UUID=cd90e23e-44ba-4626-9af0-f0b55875e4a7 /var/log btrfs subvol=/@log,defaults,noatime,compress=zstd:1 0 0
tmpfs /tmp tmpfs defaults,noatime,mode=1777 0 0
I think this is the log from my last broken boot:
I mean, it says Started Display Boot-Time Emergency Messages In Full Screen. In one of the lines.
So I ran:
sudo pacman -Scc # Confirm with ‘y’ twice
sudo pacman -Sy
pacman -Qqn | sudo pacman -S -
Still emergency screen, even for lts.
The reboot starts at 2026-02-28 21:26:50
I’ve attempted another go today and tired to look through the log to see if I can figure out at what point during the boot the crash happens.
So, can a boot crash so hard it creates no journalctl? Because that’s how it seems to me. I took careful note of the time and that whole sequence is just missing. I only get shutting down after updating and then launching from snapshot. Am I at the point when I should actually just scrap the system and install it anew?
So, I’m still fighting to fix my system. I’ve tried both adding to an existing arch system and removing Cachy repos per the wiki, both result in emergency screen. I’ve rechecked and fixed my pacman again.
I thinks at this point, I’d opt for a re-installation of the system. Don’t mess around with the repos next time, just go with a regular “wipe all install all” approach.
After all your tinkering, what messages do you get when using sudo pacman -Syu?
Sorry, did not see your log from four days ago.
You said in the beginning that you were used to running rate-mirrors, but how did you use it exactly? Did you ever try using cachyos-rate-mirrors instead?
Edited:
Wait, did you accidentally edit this part before posting the fstab content?
Was it really on two different lines? And I am still very new to all of this, but should it not be subvol=/@root, following the same logic as the other lines?
Yeah… I’m gearing up for that. I was thinking a lot about how I got to this point anyway and I think it all started with me struggling to run the installer in the first place. It took way too many attempts the first time I tried to install, resetting keys and all, desperately, over and over. Something, somewhere, must have messed up back then, because the subsequent updates never worked for me. That’s why I messed with the pacman.pacnew since I thought that must have been the problem the whole time.
Any advice/article I could refer to? I’m already tasting the 18% crash during install again, lol. Pretty sure it was time outs. People were fixing it by resetting keyrings through the console but I have no idea if that was the right approach in the first place.
All and all, I’m still impressed, because the Cachy-spice Arch-mess I’m running actually runs extremely well. Sound, bluetooth, games, everything is perfect, except I can’t keep the computer securely updated.
I’m sorry if I wrote that wrong, I’m sure it was always cachyos-rate-mirrors.
I never ever touched the fstab except for opening it and reading the text. I’m open to try and fix something. I’d absolutely need exact instructions on what to do tho.
Edit: checked the fstab again and the root looks to be in one line. It just posts weird.
I am not the right person to ask how to fix something like that, but good to know it just ended up looking weird when posting it here.
Did you try the “install all packages” option yet? It does not sound good that you have been having issues since you installed everything to begin with. That is definitely not the experience you should have from the very start. Do you remember if you validated the ISO integrity before you started?
Oh, I see the “reinstall all packages option” in the Hello. I’m pretty sure I’ve run commands which do that too, but I can try this now that I know about it.
I did not validate the ISO. How can I do that? I guess that’s the checksum but I don’t know how to use it.
I downloaded the ISO again.
I verified it using the guide.
Wiped drive completely, installed again.
So far, everything seems perfectly fine 
That may have been the ‘solution’ to your added ‘why is everything broken now’ (which in turn means something else was broken deep down though we do not know what) but the original ‘unable to run system upgrade’ solve to the thread title remains the same.