Our customer has been with the bank for years and it is a great banking relationship
many a fraud story starts with this very statement. not meaning to imply that this in any way is fraud, but it sure opens your bank to potential for liability.
you've identified potential risk, so you can either refuse future deposits until it gets fixed - and i think your client would work much harder to have the maker write the checks correctly if they are refused for deposit - or continue to accept and take on risk.
and of course, Randy's suggestion of engaging counsel is sound.