For example, assume item is marked as lost (and fines are voided and a lost fee is applied). Then later the item is returned, but is missing a disc or something. Staff does Mark as Missing Pieces. Part of that functionality is to renew any existing circulation or open a new one for the patron, the rationale being to give the patron more time to find the missing piece. This already fails in that renewals on lost items are disallowed, so there is no time extension here. Then, normal resolution for both lost and missing pieces is to check-in the item. However, if the org unit setting circ.missing_pieces.copy_status is active and changes the item status from Lost to something else, then normal lost-item handling will not happen on checkin (depending on settings, this would include re-instating fines and voiding the lost fee).
Maybe the fix would be to disallow mark as missing pieces depending on the item state, or otherwise force resolution of the Lost state first.
