Hey, I had this issue before on my N3ds, so I downloaded mGBA for it and it's been working quite well. It feels like it takes more battery and sometimes the gameplay stutters so it lags and the music plays slower, but only in certain sections and not for long. I tried making a .cia file before but I was just faced with an eternal "white screen" and I think I read somewhere on the internet (could even have been Resetes) that it means that the "emulator" isn't good enough. I actually just installed another romhack called "polished crystal" today and that I could install internally through a .cia file, but when I ran it the first time it said that my emulator was not good enough, that bugs would appear and that I should run it on mGBA or another equally update emulator instead, but it let me start a new game at least.
To Resetes: Today was also going to update from 1.3.5.3 to 1.4.b but now it seems I can't continue on my save from 1.3.5.3 since when I launch with the old save files (both the .sav and .ss0) the game freezes on launch. It seems to work fine if I start fresh but I'm not really keen on that. Is this intended or am I messing something up on the way? Tried patching the same ROM with both JS and FLIPS, same outcome both times.