I don't know about the transaction window. Never used it. If it works, forget everything below.
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I think what I would do is go into the reconciliation window, and reconcile the checks (they should appear there). Leave the reconciliation window by typing POSTPONE.
Then, I would re-enter the checks in AP, and post them in AP and Fund Accounting. Then, I would void them. Then, I would reconcile all three transactions (the original check, the new check, and the voided check). You now have a record of the voided check.
Lastly, I would make a correction entry on the beginning balance for the amount of the checks:
DB 01-1110-000 checking $_amount_of_checks
CR 01-3110-000 net unrestricted assets $_amount_of_checks