You may already be aware (sorry for wasting your time if you are) but the normal process would be to move stock that is to be scrapped to an interum storage type (or pull from an interum storage type creating a negative there if adjusting up). Not to clear differences directly from the source storage type.
If moved to 999/Lost&Found you can use transaction LI21 to post the inventory clearing for multiple items at once so it not much more work intensive then scrapping manualy with MB11 would be.
Personaly I see some risk involved with allowing the clearing of inventory differences directly from bulk storage.
recoment to use LT01 to move (or pull) the stock into (or from) 999 and clear the difference with LI21