This makes no sense. The deducted amounts were sent to a closed account, which means that they were never accepted or credited to the named account (now closed). The money is either still in the employer's Accounts Payable (Payroll Payable), just like any uncashed check, or it is in a Suspense Account at the entity which provided the HSA account. This is just like any other check that is not received or is not cashed. The audit trail is similar and there should be no problem in finding out where the money is, since the are only 2 places where it could be.
Since this is a salary reduction done through your cafeteria plan and subject to those change of election rules. Closing the account to which the funds are to be deposited does not cause a change in election. The salary reductions continue for the election period.
Where do the funds go, now that the original account is closed? I suggest that you inform the employee, in writing, of the requirement of an account for the deposits. Usually, I see an agreement between the HSA holder and either an HSA Bank or Administrator. This agreement would give instructions regarding what to do in a case such as this. Usually, an account can be opened on behalf of the HSA holder. Have you seen any such Agreement? Have you informed the HSA Administrator of the situation?