So for a while my JCM 2000 has had no problems, but I accidently plugged the output of the preamp into the input of the amp and I couldn't figure out why my guitar wasn't working (for those wondering, I wired up my pedals wrong and that's how it happen) and so 15ish minutes later i figured it out and plugged it back in normally. I didn't notice any difference but could this of done any damage to the preamp section?

And yes...I feel dumb for doing that
you are fine. it just instrument or line level.

now if it was a speaker cable to the input, you would be having some problems.