An AUP is treated as an ancillary (like baggage) so is issued on an EMD-A document, not as a ticket - confusingly though, they have the same type of number so you wouldn’t necessarily know unless you looked at the receipt. Anyway, EMDs don’t earn any Avios, which is why it was rejected when you entered it - you would have travelled on the underlying original ticket. Conversely, an upgrade purchased in advance of travel is processed as a reissue of your original ticket. If you kept your boarding pass, however, this would have the correct ticket number printed on it and this is the easiest way to claim.

(This is actually one area where BA’s IT is much more advanced than many airlines, where AUPs don’t earn points because the system only picks up the underlying ticket not the EMDA, but BA has built a process to look at both together for their own flights.)

Call centre waits are short at the moment though so you shouldn’t have to wait long.