@MCCM
Record a deposit for the amount of the stale check into the checking account and assign it to a temporary clearing bank account (set one up if you don't have one). Then, write the new check and assign it to the same clearing account as the deposit you just created. This keeps the stale check in the closed period and the new deposit/check will net to zero in the current period.
When you reconcile the bank account, clear the stale check with the new deposit and clear the new check when it clears.