Yea I know it sucks hard when you loose data like that. But you have to think of the GMS2 generated project folder as exclusively belonging to GMS2. As you add/rename resources, folders/files get renamed, deleted etc. It can do whatever it needs to do inside that folder to maintain project integrity including removing redundant and orphan files/folders. Version control + local & remote project backup for me. Can never be too careful. I think all of us, at some point has endured the very painful lesson of data lose. Sigh.
Heck I remember when I got my 1st virus way, way back in the day. The little bastard attached itself to the boot sector and would not go away. I will never forget the day, I turned on my machine and saw the message, your machine has been infected by "blah blah" (can't rem the name) virus, now turn this piece of crap off (this was the actual msg shown). OMG... I freaked. Long story short, had no protection and hadn't made any backups... had to reformat my HD to get it off. DOOH! Haha, ran out and purchased Antivirus for the 1st time (never had a problem up to that point so the mindset was... meh.. I don't need it. Yea right).
Anyway bro, it happens to all of us. Force yourself into the discipline of making good backups. Make some batch files or use automation software to do it, but most importantly do It NOW!. Yea I know... in hindsight right?.