I called Mileage Plus on the matter of the missing Sep flights again. Spoke to an extremely nice and helpful Denise Peel, who checked with a supervisor. After a few minutes, she reported that they could not submit a duplicate flight report to Hilton, but that they would credit me with enough MP miles, such that I could transfer them to HHonors for approximately the missing miles.
Today I received a call from a MP supervisor (Misty), who confirmed that they would be posting the miles to my account. Only problem is that the tranfer to Hhonors is done only in 5k mile increments (to 10k Hhonors points). Since I was missing 16k Hhonors points, I settled for 5k MP miles.
I was very surprised to be called by MP. Looks like they are taking this customer care emphasis seriously.
I will also be sending an attaboy certificate (forgot what the official name is) to Denise. If UA could figure out how to clone her...