May be realted to bug that causes disappearance of items being swapped without having a compatible inventory solution. For instance, dragging a Longhorn from pants pocket onto Amphibia in chest holster; since chest holster will not accept Longhorn, the Amphibia takes place of Longhorn in pants, but Longhorn is either discarded onto ground, or lost completely.
I'm not sure how much desync has to do with this, but I have scoured (flat) areas of lost weapons to confirm their absence on a number of occasions.