<Does that cancel out the short position in the MM's books, even though a real share never changed hands either going out or coming back in?>
1) broker/dealer sells short...assigns a cusip to an imaginary cert, brokerage account shows a credit for the shares, short seller receives money
2)broker/dealer covers short...brokerage account debits the shares(real or fake), short receives the bogus share back, shares are destroyed, books net out
3)DTC keeps their eyes closed and their hands out...