As a suggestion, and I'll start with a disclaimer I don't entirely understand the facts of your situation. Since your first inquiry went nowhere, rather than informally communicating, move on and file a formal missing stay credit request. Perhaps that would result in either credit or a clear reason why it is being denied.

The old rule of thumb was if your travel agent just made a reservation in your name and you paid the hotel with a card in your own name at time of stay, it was a published rate and you received credit. But if you paid the travel agent you would not. But things have become much more nuanced. If the travel agent contracted in bulk and passed on a reduced price even though you paid the hotel; then maybe not.