The current version lets you save resolutions but is less compatible with games that were previously working.Is there a retro arch version that lets you save the resolution yet?
https://gbatemp.net/threads/ripping-the-nes-virtual-console-palette.371706/
I also have my own version based on 1.0.0.2 that lets you force a resolution at startup but you need to write it yourself in the config file; 'video_vres' 0=512x192, 38=640x480, etc. You can find the link in the op.
If you end up trying my builds check for the input sticking bug, I recently added a fix for it, would be nice to have proper confirmation that it is indeed fixed because it is definitely fixed for me.