If you connected the output of the TC electronic Flashback 2 effect pedal into the output of the headphone connection on the rev2 by accident would this do anything? From memory, I think I may have done. So essential you have an input going into the output headphone connection...?
Yeah, I think it could... Headphone outs have quite low impedance, as do headphones, but line outs have a LOT higher impedance. I'm not really a techy guy, but if I recall headphones have about 8 ohms to 600 ohms impedance, line outs are generally 10k ohms or more?
Probably a bit like plugging two water pumps outlets together with a hose, pumping water AGAINST each other, one pumping at a pressure of 1 (representing low impedance, say 10 ohms), and the other at 1000 times that pressure... Guess which pump will break.
Just a guess, I'm absolutely no expert on this, but I think you may have accidentally damaged the headphone output. I doubt anything else would get damaged, and that it would be a relatively cheap and easy fix. But that's just speculation.