Besides the FOD, there's also the opposite. Another reason for accounting for all parts and tools. Missing components after maintenance or even construction have likely caused many crashes or close calls. You know, "Hey, Joe! what's this bolt for?".
And that's what happened to me on the infamous leading edge flap failure. Thru the grace of God and that FBW system, it would have been a lawn dart when right LEF folded up about 200 - 300 feet in the air on takeoff.
The folks working on the flap system failed to insert and secure a "keeper bolt" that kept the drive motor shaft inserted into the flap drive tube that ran the length of the wing. So the "spline gear" connection worked itself loose on the way to the runway and came disconnected a few second after gear up. No procedure for the failure, as this was early in the plane's history.