I just wanted to document this for other people who may encounter the issue and also for the CachyOS team, since this could be a bug with the installer.
I will try to be concise.
I have a machine with two bootable drives. Both NVME. The primary contains my Windows 11 LTSC 24H2 installation, and my secondary my Linux installation. I had a working configuration this way with EndeavourOS using systemd boot.
I decided to clean install CachyOS over my EndeavourOS. My drives are easy to tell apart, since my Windows drive is 1TB and my Linux is 500GB. Also one is Solidigm and the other Samsung.
After wiping and installing my Linux drive, my Windows drive was no longer bootable. Upon examination it had no EFI partition and so was not visible to BIOS. I also couldn’t mount it in CachyOS, though a storage drive with NTFS formatting was mountable.
My resolution was to shrink the primary partition on my Windows drive to make space for a new EFI partition, and then to make it bootable using Windows recovery tools from a live USB (diskpart and bcdboot). This way I was able to regain access to my Windows install.
This seems very peculiar to me. Could CachyOS have deleted my EFI partition on my Windows drive? Why was there no free space on the drive for an EFI partition? It can’t be a coincidence, I’m just not sure by which mechanism this happened. The only thing I could think of is that my EndeavourOS install had the boot information for all drives, and removed said information for the Windows drive (i.e. deleted the EFI partition), but I don’t think that makes sense.
From Google, I was able to find one redditor with a similar problem, but they weren’t that knowledgeable, and resolved by reinstalling Windows.