Proton games don't run after removing and readding the GPU via /sys/pci

System Information

• GPU: NVIDIA GTX 1080 + Intel HD Graphics 530
• Driver/LLVM version: nvidia 525.89.02 + Mesa 22.3.5
• Kernel version: 6.1.12.zen1-1 (Arch Linux)
• Proton version: experimental-7.0-20230227 (and any other tested)

Symptoms

/sys interface and "replugging" it with PCI rescan until the next reboot (they work correctly otherwise).

Use case: I want to be able to use the dedicated NVIDIA GPU in a VM using VFIO and without rebooting. To this end, my base rendering in Xorg is done with integrated GPU, and for Steam and Steam games I'm using NVIDIA card through PRIME; so I only need to turn these apps off in order to be able to use the dGPU in a VM. To return the NVIDIA card back to the OS to use it with PRIME again, I am removing it through the /sys interface and issuing a rescan command. After doing so, rendering with PRIME works again for native apps (tested with Valheim), but Proton apps don't run correctly. Logs from an example run (tested with Noita) attached - steam-881100.log .

Reproduction

1. Set up the OS so that it uses the Intel card for base rendering and use NVIDIA card through PRIME for Steam and Steam games.
2. Remove the NVIDIA GPU and then rescan PCI:

# echo 1 > /sys/bus/pci/devices/0000:01:00.0/remove
# echo 1 > /sys/bus/pci/devices/0000:01:00.1/remove
# echo 1 > /sys/bus/pci/rescan

3. Try to run any game using Proton, which should then fail to start.

Start by reproducing the PCI removal and rescan sequence with the listed Intel/NVIDIA, kernel, and Proton versions, then inspect the attached steam-881100.log from the Noita run. Compare Proton behavior with the native Valheim result; done means Proton games start correctly after the GPU is removed and rescanned.