Decided to try a few things before replying to you again.
I noticed that SD Maid was, in fact, NOT actually deleting the folder as I had thought. So I decided to use ADB commands via my PC to really delete the file. I was able to confirm that the folder was being deleted properly via the file explorers on my PC and my phone. After that, I restarted my phone, and ran Mupen FZ again.
It loaded into a black screen yet again. I checked the filesystem to confirm that the broken folder is back.
At this point I have a weird hypothesis. I noticed that the name of the folder shows up in my ADB shell as:
0.11 Dev LĒTHERS (U)
This contains some odd characters that are maybe causing some sort of conflict. Maybe Samsung phones don't play nice with weird characters, and this causes some sort of issue when Mupen tries to read it?
So here's my question, what's a good way to change the header/title of a n64 rom? If I can change the name to something else, so that Mupen reads it as a different game, and thus, creates a differently-named folder, maybe that will fix my issue?