Hi,
Well, the screws ought to blow right through the engine, as they're small and it was wide-nuts open at the time. The butterfly plate is a bit more worrisome given it's size.
I'd expect it to get stuck in the intake port for one of the cylinders. I think the intake is smaller than the butterfly. It might well deform during the process, though and wind up getting stuck at the valve. If so, then that would surely make a sound!
I can't see it going past the valve, but then I have see odder things happen inside engines. Mostly racing engines, for sure, but I once saw a mechanic's fender pad go right through a 720 diesel that wound up runaway on it's first fire-up aftrer a rebuild. It was tossed onto the intake to stop the thing, and didn't work. That same engine deformed a 1/16" aluminum plate which was slapped over that intake right after the fender pad came out the exhaust in flaming pieces.
The plate did work to stop the runaway before the thing grenaded, but half the fender pad wound up stuck to the rafters still on fire. That was a pain to put out before the whole shop went up....
Anyway, if I found a butterfly plate missing, I'd surely go looking for it until I found (a) the fool thing or (b) did not find it anywhere in the intake or exhaust tracts and manifolds or inside of a cylinder....
As to the knock and what it is, if I were missing a butterfly plate and then the engine started knocking, I'd certainly figure that the missing plate likely had something to do with the new noise!
I'd just yank the manifolds and head and take a long, hard look at everything from point A to B to see just what happened when that plate went missing.
Oh, and I'd probably find a few things to repair along the way. Like a bent valve or maybe even two if the plate mangled it's way past the intake valve and through the cylinder and into the exhaust.
If you feel adventurous, use a mechanic's stethoscope to listen to the thing running as a slowly as it will run and see just where the noise is coming from.
later!
Stan