You can re-run the Gift Deposit Form, however the earlier processing would have created a transaction in the Check Reconciliation process. You can simply delete the original transaction in the Check Reconciliation, then re-run the Gift Deposit Form.
Each time you run the deposit form for a checking account you are presented with the option to send a summary transaction to the checking account reconciliation in AP. Each time, believing this is to be the last time, you answer yes. Of course this will result in multiple entries in the checking account transaction list. It is best if you delete the versions of the deposit that aren't needed as you create them, but there is no harm in waiting until reconciliation time.