I'm confused. You said it fell into this area in another post -
"A bolt went here inside, is any problem if i run the bike with a bolt inside that tube where you adjust the chain?
"
That suggested it went into an opening in the swingarm (which I didn't think there was).
Could it be sitting on the inside lower lip of that bracket? Not sure where else it could go?
I don't think it would cause the problems you are experiencing here -
https://www.ninjette.org/forums/showthread.php?t=311931.
Anyone following this better than I am?