Then you should use a separate memory card solely for retroarch. The app crashes that frequent and also the dev who made the app even advised to use FAT32. I have left retroarch for the same reason you mentioned. My exFAT memory card also got corrupted during the use of retroarch. I had to recreate my emunand, reinstall all my games etc. Two choices. Use retroarch, format to fat32 and not get corruption. Second, don’t use it. If you use exFAT you will get corruption again.
I really do believe my corruption stemmed from me updating it on the Homebrew Appstore, despite downloading it online. It might have mixed up files. Speaking of, well Ozone loaded successfully, activating the overlay menu (START+SELECT) crashes Retroarch exclusively in Ozone, so if I ignore that particular driver
(despite how much better it looks), then it runs just fine.
Also, another problem with FAT32 is that, once we can emulate Wii games, which we should be able to because the Joy-Cons have a gyro that can simulate the pointer and all the functionality of a Wiimote and Nunchuck, they will exceed 4GB and then I'd need a separate card for Switch and Wii games, which will of course exceed 4GB in size. I doubt the Switch will emulate Wii U, so that's not as big of a deal.
The last notable thing is being able to backup my NAND. I suppose that would be the primary reason to just get another microSD (64GB should be fine) so that I can get NAND backups onto the PC safely without having to pile them all up together again, which was a difficult process if I remember correctly back when I did it when I used to do NAND backups with my FAT32.
Since I have been able to conclude my current problems with Retroarch began when I installed an update from the Homebrew Appstore, exFAT has not played any role in this at all. In fact, almost everyone here mentions exFAT, yet they were not as quick to get to the root of my actual problem as crazy_p did, who said I should switch to FAT32, but was not making it the main point of his post.
That is, unless somebody is going to mention the update being installed on exFAT is the reason why I had to remove my CFG file, which would make sense if exFAT has trouble writing data. I suppose I can just buy another microSD for Wii and Switch game emulation since, even though I presented an argument as to why I should keep exFAT, I came to realize its only true benefits are with files that regularly exceed 4GB, which the majority of mine do not.
So, after extensive thinking, I may just change my format to FAT32 after all. Well I seemed fairly antagonizing at the start of this post, I was thinking as I was writing and came to the conclusion FAT32 is overall more beneficial. So, thank you to everyone who presented their arguments as to why I should use it. I suppose peoples' opinions can change overtime, because I remember a lot of people saying I should use exFAT, but now it is FAT32 and I suppose that is maybe because, according to what I have read here anyway, nobody realized the exFAT driver in the Switch was bad at the time and now they do. That is the theory I believe is why everyone is suggesting FAT32 nowadays, even though it was definitely not the case a year ago.
Again, thank you to everyone for helping me out. The last notable problems I have left are Ozone disappearing from my driver list every time I change out of it, some of my setup playlists saying "File could not be loaded from playlist." despite setting them up correctly and Ozone's overlay menu (START+SELECT) crashing when I try to use it in-game to exit the game. I know Ozone has a lot of problems, but I would really love to have it as my preferred GUI because of the fact the aesthetic is way nicer, complements the Switch much better and I really enjoy how it sorts everything. So, I hope these are problems that can be addressed. Though, if you'd prefer I make another thread about it, I can do that.
