Ok. First, I would'nt modify the lower assembly. Nor recommend any one to try doing so in the future. Its a recipe waiting in disaster, unless your super confident you have an understanding of what your Mods will do in Off set weight transfur. Tho Its a small motor, you should be ok as the reciprocating assy isnt going to be stressed from fluctuating rpm's or load limits.
Your counter ballancer will act as a weight to equal out and eliminate harmonics from your upper assembly. All this will cause vibration. No two ways about it. It can be machined to a degree but it will always exist some where. So likely If all checks out, as Herb above had pointed out. The bolt may just have come loose from Vibration. As said, Lock-tight will help prevent it happening again. Just clean the area to a degree you could eat food off it, and glue that pesky bugger back in there.
Squishy gets a slap on the wrist.
Dan