There are 2 note in which SAP says "In a stock transport order-related SIT scenario, it does not make sense to enter a difference quantity in transaction VLPOD"
Please read: Note 1650505 - Error message M7264 during SIT postings in transaction VLPOD
and Note 1682012 - SIT goods movement using POD IDoc (message STPPOD)
There is some more info about the standard design
Try if you can use 304 movement in shipping plant to get the 2EA material back, then do a 551 scrapping