When this is the case, then the Indiana Department of Revenue has recalled the warrant. You must send the payment to the DOR. You should endorse the check but also write on it that this is for deposit only by the Indiana State Department of Revenue. Mail the check to the DOR. Also you should send a letter to the taxpayer saying that you no longer have this warrant, that the state DOR has the warrant, and that the payment has been forwarded to the DOR.
You could also receipt the check into your cashbook, then immediately cut a check for the Department of Revenue and mail it to them.