Similar thing happened to me yesterday. Booked a long haul award return flight 4 weeks ago for a relative, payed with AMEX , I approved the payment, booking confirmation with booking code issued. I was able to log in to the booking (manage booking) with the 6-digit booking code and select seats. Avios deducted. So I forgot about that, I gave the email and phone number of the relative in the booking. Now the time for check in comes- and my relative was not able to log in to the booking and did not find a confirmation email. I checked my account, avios and still deducted and there was the 6-digit code booking code in the history.
So we called the Qatar help center- where they tell us the payment did not go through. . As AMEX was used and I confirmed the payment, I could not imagine anything wrong with it. During the same call they refund the Avios without me accepting that.
I call AMEX, they said Qatar denied the payment ?? I was never notified of the payment issue. Called again Qatar, they refuse to do anything, don't want to rebook on the same flight, only option is with considerable date change. Of course Avios points for the same flight are tripled already, prices are high.
I am preparing now the complaint- they obviously have a glitch in their IT process, reading the thread I am not the only one. I am a frequent traveler, however I have never came across the rule that the booking confirmation , and being able to log in to the booking is not a guarantee for a flight. Moreover they did not refund the avios the whole time.

Very skeptical they will reply before the time of travel, so this will result in buying last minute tickets otc at a high price. Do you have any suggestions how to proceed besides of the complain? 2 of the 3 help center employees were extremely rude and unhelpful ( another thing which bother me as a status member), the one which helped can not rebook flights.