To replace a stale paycheck, or any type of check, all you really need to do is to record another (standard) bank check in your bank account, and then use the bank account in the detail area of the check.
This will create what looks like a check and a deposit in your bank register. Perhaps add a memo to it explaining what it's for.
Then, optionally, perform a fake reconcile: Make the ending balance match the starting balance. Then mark the old check and the "deposit" line of the new check both as cleared. The reconciled net total will be 0.00. Then perhaps print the reconciliation report and put a note on it, explaining what you did, for your records.