If all items on the deposit window have been deposited in 1 large group, and the actual deposit was done in multiple smaller groups, the best way to fix is as follows.
1. Decrease Cash in Bank by the amount of the large deposit. Post against a temporary or suspense account, for the date of the deposit.
2. Enter separate transactions to Increase cash in bank by the amount of each deposit, pulling from the suspense account. When done, the balance on the suspense account should be zero.