Save states are not always portable between emulators, so a save state from lr-gambatte might not worth with lr-mgba . Is the emulator version the same as the one you used for the save states ? Sometimes an upgrade of the emulator makes it incompatible with previous versions' save states.
Hmm maybe it's because of an emulator upgrade. I played the game for a couple of month before I did the backup. And after I think I did an update. Thanks, I did not know it might cause a problem. At least the "normal" save file works.
Nice troubleshooting. These types of problems with RetroArch turn up often when 'Save Configuration on Exit' is enabled, so be sure to make those files your first port of call for any other inexplicable issues going forward.
Just as a point of interest, any creative intellectual work is automatically protected by copyright when it is created under US law since 1978. This would obviously vary from country to country, but the patches in question would indeed fall under protection in certain areas of the world. One particularly relevant violation that comes to mind is a limited print run of 'Cheetah Men II' that utilized a fan-made patch from romhacking.net without permission for monetary gain. The people responsible actually owned the full rights to the game and the accompanying intellectual property, so I imagine they just assumed they had the right to use the patch as well.
I solved the problem. Like how I caused the problem, I don't know what actually fixed it, but I went into the... myriad of config files, from the command line and from the configuration editor in EmulationStation, setting the shaders to "false" as per your suggestion and this fixed things, only the GB games were black and white instead of green and worse green. But I solved this in the quick menu>options>BG Colorization custom and >Internal Palette GBC - Green, although that second one may not be necessary.
The kicker is the game I've been playing, in monkeying around with stuff, I wound up making additional config files for this specific game, so it was still green(!) I used the File Manager in ES and went to /opt/retropie/configs/all/retroarch/config/Gambatte and deleted all the .cfg files except Gambatte.cfg, which was the file I had edited earlier to fix things (I think). But it works now and I'll leave these shaders and things alone for a while until I'm ready to make another big mess.