Originally Posted by iknowthings

A lot of hotels, especially those not within the US, use a third party marketing company that, for whatever reason, sometimes removes your Bonvoy number from the reservation in the Central reservation system not long after it is booked. This causes the reservation to dissappear from your Bonvoy account. When the hotel's system starts the online check-in process a few days before arrival, the hotel's system reconciles with the central system and re-enters your Bonvoy number and the reservation again becomes visible within your account.

Basically this is one issue that is not the fault of Marriott IT but rather the hotel for utilizing the marketing service that is doing this. It's rarer in the US but not impossible. The central reservation system itself never spontaneously removes Bonvoy numbers, it has to be done by an outside source.