Ok, so I found the file vfio-pci.cfg under the config folder on the USB flash drive. It contained a line starting with BIND=, followed by these IDs that I listed above. I just deleted that file, and the server booted fine. I have a copy of that file just in case, but it seems no new file with the same name has been created. I'm assuming this binds the GPUs to certain IDs? Anyway, my VM with GPU passthrough is working like before, and server is thankfully doing fine.
