I'm in the same boat, man. The game wouldn't spin up for nothing a couple a weeks ago; so I reinstalled and cleared the game files from the "my documents" directory as per much the advice I'd seen on forums and support. This fixed the game but when I was able to get it going, all my perks were reset. I don't know if what I did caused the issue, but I dont think it did; my first assumption was that it had something to do with EGS because I had seen a lot tech problem threads with it since the game was released on EGS. After reading through forums and the KF2 support knowledge base, I dont think it's just to do with EGS; I've read threads about this happening on all platforms. I've put in a ticket (2 actually, because I wasn't sure if I had submitted the first one correctly) with Tripwire; so far, I've just got the auto generated acknowledgement emails. Unfortunately, I've read some pretty disheartening threads about it, haven't heard any hopeful stories from people I've talked to about it while playing, or seen any good news on r/killingfloor.
Theres been a lot pretty big issues lately; plus the Halloween release coming up, so I reckon they're probably swamped right now, but I'm still hoping they can help us out... Ive got a lot of time and effort into leveling up all the perks, so I could pull my weight in the higher challenges and play the game the way it was meant to be played. Right now, it's lookin like we're kinda SoL, though.
If I hear anything one way, or the other; I'll post an update here.