Update regarding the "corrupting mod type of thing:"
So, I am working on two projects at the moment here. I am working on a whole new mod (something that is NOT "CSBB") and another mod where it IS a "CSBB." Let's focus on the "CSBB" type of mod:
Each time I finish modding modding (like, the executable of the game for example), I always test the game to ensure everything works smoothly. Once it meets my satisfaction standards, I feel proud of myself and move onto whatever other task I have thereafter. At the end of the day, I power off my PC (or Virtual Machine, in this case) and do whatever else, like heading to bed. The next day I go to edit my mod (the executable, again) again, CaveEditor just crashes. Why? Because discovering by going into the game's directory, I notice that the game has absolutely no icon, and executing it will alert you that it has been corrupted (additionally, DoConfig still has an icon). It just seems like that every time I power off my machine and boot back into it, Windows just corrupts the entire game (not the files, just the executable). I am not sure why, but a majority (~20) of my mods, that are stored in the same folder (Documents), are still perfectly fine. I have absolutely no idea why this happens. It is extremely unlikely that using a Virtual Machine will cause it to corrupt it; my other mods are perfectly fine, and they would have been corrupted by now if that was the issue.
I have not tried another machine other than this machine, but I already have the same expectations. I use a Virtual Machine specifically because I choose to not install any games onto my new, main PC. I do, however, have another machine, such as a laptop, that can run Cave Story (and CS mods), but it does not have great performance and can cause applications to lag because of its old processor, and its storage drive (HDD instead of an SSD).
So, I am actually out of ideas. Running the game in Compatibility Mode will not do any good, because the game is already corrupted. I have made several backups stored, but those got corrupted as well.
Any help is appreciated, though.