Hi,
Doesn't the confirmation letter mention the "effective date of confirmation" as the actual due date? If it does, then it is fine to keep the letter with him, as company still has right to void the confirmation, until the due date. If matters do not come to that requirement, then at least you make the employee happy.
If you have put the "effective date of confirmation" incorrect while issuing the letter, or it is not mentioned in the letter; then it would be better to either make the decision to keep the confirmation valid from the date of issuance of letter, OR to take the letter back.
Regards,
Amod.