by Brian Crow:
This is governed by your state's Uniform Commercial Code and your deposit agreement which should specify timeframes for your customer to identify and report an error and the bank's liability for honoring an item that was not properly payable. If you are not sure how to interpret the law or your contract, you should ask your legal counsel to review.
by John Burnett:
If your bank honors its customer's claim for reimbursement when the UCC and/or your deposit agreement provide that the customer's claim was late, you will likely have no ability to collect from any other bank involved.
While I totally agree with Brian -- you should consult legal counsel -- if your customer failed to notify you until more than a year passed after the statement was sent showing the second payment of the check, you should be able to tell your customer he was too late to the party, and suggest that customers have a responsibility to check their statements promptly for unauthorized items and alterations.