I believe I've figured out the issue. The issue was with me, if anyone. I was using git version control to see what changes were being made between versions because I noticed most of the data was in text, and it interested me greatly to see what you were doing, and I may have tried switching versions via git and apparently something isn't being versioned/replicated correctly when I'd switch versions and it caused the game to see all these issues, whether they were there or not. My apologies for wasting your time. ;-;
Scratch that, something is happening without any interaction from me when I close the game... And I don't understand what it is. Git doesn't pick up any changes to the mod. I'm so confused... For context, I've added a screenshot.