Pretty much the only thing you can do is what we had to years ago. Don't touch payroll, do this in the General Ledger.

Make a GL account for stale/write offs. It doesn't really matter if it's a payable or an expense account if you're going to pay out the money, but for ones that may not be reissued, an expense account may be easier to have them all in one place. Make a GL entry to move the money from your outstanding cash account to the new stale/write offs account. On your reconciliation, mark both the check and the GL entry you made to get the check(s) off your reconciliation.