I lost a bolt into the carb of an old Cobra Snow sled (back when they had no aircleaners, just a rubber horn sticking out there. We tried to make a homemade air filter setup, which included a bolt and a nut, that later came apart from vibration, and got suckked in while doing 8,000 rpm. It was a two-stroke engine. It smashed the skirt off the piston and scarred the crankcase up a bit. (And made some major noise.)
After fishing out all the broken pieces, we put her back together with the damaged parts and run her for a few more years.
Thankfully I learned my lesson on an old pelter.

I feel for you on this predicament there buddy, I hope yer bike is not damaged too much, maybe the nut is only stuck in the intake valve... ....HOPEFULLY....
If nothing's bent, you can easily run with a couple of dents in the piston or head.
Good luck on things, I hope it all works out.