That's very weird. Try downloading it again, might be your antivirus erasing stuff. (Happens in RPGM games, havent seen it happen in SRPG Studio games)
Ah, it could be since I'm trying to run it on Mac through RPG-Maker-Launcher. I got to the last chapter then had some issues with virtualization i'm unable to resolve, so I'm trying to find ways to play it natively on Mac, also hopefully without installing wine. LMK if you have any thoughts on this, or rough equivalents I could try.