A FINAL UPDATE:
I guess they are finally catching up, but I got a call back from my week ago escalation to engineering about this issue (that is now fixed). I'm posting this because it might help someone else who has the same problem in the future.
I asked about the flag that was removed and he told me that he didn't know anything specific about the flag or how to manually remove it. However, he said that he does know that the system looks through all the accounts for any with older MPG boxes and flags them. He went on to say that the flag removal procedure is supposed to be an automated in that when an upgraded DirecTV receiver replaces the older MPG receiver it automatically removes the flag.
This makes sense because originally we didn't have the pop-up message on the origional Hughes GAEB0A (APG) receiver. However, when we attempted to activate the upgraded D12s and they 'rebuilt' the account the GAEB0A somehow got listed as an being an older RCA (MPG) receiver. Once the system set the flag for that receiver (or access card, or whatever), it appears as though it was waiting for a DirecTV receiver to be swapped out so it could remove the flag. However, due to our unusual circumstances, we swapped it out with a later Hughes box. Apparently the glitch is that the system won't automatically remove the flag for other brands of receivers, despite the receivers not needing to be upgraded. At least this is making some sense now.
Thus, I'm assuming that my coworker's solution of them keying into the system that the Hughes receiver is a DirecTV receiver and then use the Hughes RID number and access card number, would probably have automatically cleared the flag. The only problem is that I heard from a couple of sources that while this is technically possible, finding someone who can make the change wouldn't be easy. I believe this because, as I mentioned in previous posts, I tried to change the "product line item" (as peds48 called it) and customer service reps would tell me it was done, but it would never seem to sick. It ended up taking some serious work just to get the incorrect RCA information changed.
Again, thanks to everyone! I hope someone else will find this information useful.