Patience. It will work out. Other than the additional time you will spend, as long as deposits were timely received, there should be no problem. Returning the check makes sense, to reduce the chance or underpayment dunning.
My customers get notices, usually referring to deposits, where something was applied incorrectly (by the employer or the IRS). Same for forms which were never received, even though there is proof of filing/mailing/receipt.
This is one of the reasons I encourage all employers to make deposits every payroll, even if they are not required to. If an employer needs to "use" the trust funds for operation, they need to resolve that issue anyway, or they are already on the verge of ceasing to exist. Also, to never ask for funds to be applied, always wait for a refund. How over payments get applied can be as random as how payments get applied... Waiting for a refund check takes zero effort.