Ah, you are correct and I figured out what happened. When I extracted the new folder I told it to merge with and replace the old folder with the same name (Fujistory-1.0-pc). What I hadn't noticed, because I didn't think to check, what that 2.0 used Ren'Py's archive file structure (.rpa) while 1.0 used the uncompressed format. This resulted in almost none of the files save the .exe being replaced/removed when the folders merged. Apparently when running, it prioritized the uncompressed files and so ran it as 1.0