Windows 11 Boot Option Gone After Installing Bazzite

I think your problem is here, there isn’t an EFI partition on the Windows disk. Were both disks present when you installed Windows?

The reason I ask is because I had a similar issue a while back when I had two disks and Windows put it’s EFI partition on another drive entirely when I installed. So when I installed Pop OS and nuked an “empty” drive and I ended up with my Windows being unbootable
iirc, I managed to fix it by booting Gparted in Linux Mint and manually creating an EFI partition of about 300 MiB and the filesystem needs to be FAT32. I think you give it a boot flag of efi-boot or something like that. Then you can boot a Windows install USB and it should be able to repair the boot. But before you do that I’d recommend that you unplug the Bazzite disk entirely else Windows might see the EFI partition and might write it’s files there instead of using it’s own partition.