This is total bullsh**.

[toAst]

Allright, so RA2DSL was working great for a while now, and one day when I started it up, it started, but went much slower through the intro screens, when it finally got to the game it seemed normal untill I got to my teams folder. All of my 8 teams were gone but 3, and one that was all messed up with random numbers and stuff. I played normally still, and just focused on the 2 teams that worked fine, I battled Dino V online, finally got curious and clicked the number team.

KA-CRASH

Back to desktop. Well, let's try opening RA2DSL and trying that again, shall we?

No we shall not. It won't open. Game doesn't even start.

Why did this happen in the first place, and how can I reverse this without re-installation?

[DarkRat]

ouch !
Well this one is a tough one... hemm .. one problem i can think of is if the game was writing to a file at the time like say the teams or options for some reason while it crashed that file would be no more good. I have also seen while reading a file and crash in the middle of reading it can destroy it also.
But since it happend a couple of times and each time loosing more and more it sounds more serious.
I would scan your drive for a virus ASAP.

[Deceptor]

that was my idea too.......