If the flight is oversold, having a seat assignment won't really protect you from bumped. That said, I've seen a number of cases where the seat map on the AF website has shown as full, including:

• IT glitch: try again in a few hours, or a day or two later, and it magically works properly again.
• Equipment change: if they are planning to switch aircraft type or config, I've seen the seat maps get blocked for awhile until the new configuration is set in the system
• Reservation not ticketed: I used to have this issue a lot at my old company where they had a corporate agreement with AF where we could make reservations but not ticket them until just a few days before the flight. The seatmaps would show a full flight and I couldn't select a seat until my ticket had issued.

Given you had all these problems with your reservation being auto-cancelled, it would be worth checking that a ticket has been issued on your new reservation. When you bring up the reservation on the Air France website, does it show ticket numbers for each passenger?