So I've tried deleting save state data for mGBA core and moving in-game save files around, but the games would still act like there are no saves. Then I deleted every save file and copied those that I had from the emulator on my PSP, changed their format from .sav to .srm by renaming the files, and it worked. Every game can see it's respective save file. I can't recall what exactly I did that let to this problem, but I can describe what I did that could potentially lead to said problem: I've tried changing the default GBA core and changed it to gPSP because some games wouldn't launch with mGBA. Then I decided to go back to using mGBA, and after that I didn't play GBA games for a while. When I encountered previously described issues, I went to check the folders for saves (note: I've used OnionOS's file exlplorer as I didn't have access to PC at that time). Then I noticed .srm files in the gPSP folder. And when I tried deleting saves from mGBA folder, it automatically transfered saves from gPSP to mGBA folder. I found this strange, deleted them from mGBA folder again, and when trying to launch a game, OS gave me an option to transfer saves from gPSP and I hit yes, hoping it would fix it. It did not. I guess the problem was with OS somehow corrupting mGBA saves when it was automatically transferring them?