It sounds like the auditor wants to treat it as a corrective contribution under EPCRS to avoid Section 415 issues with the timing of the deposit. I wouldn't feel comfortable doing that with a discretionary contribution, but others might.
I doubt the "tax savings" of your hardship withdrawal is even close to the benefit you would have had if your retirement funds had been left in the account to generate more tax deferred income... If you do the math from the time of your withdrawal, whether you paid less in taxes when you took it out than you would now is probably a small consideration.