Days of working on the mod, fucking Windows does this shit. Unbelievable. I guess all I can do is recover most of the Stage and NPC files, along with the TSC files and copy it all in a new Cave Story directory.
Following Mister.Hex's suggestion and starting a side project to find out just what I found fun about modding.
Already collided with a few walls (namely, two incredibly lousy mobile devices) so I'll simply have to make do with what I have that I can use - Booster's Lab v0.4.5.0 and CaveEditor. (It's better than nothing, haha.)