AF operated twice a day with a 48 seat aircraft and loads were generally good 70%+ and fares were high (I'm sure OP will confirm this). I think it was Brit Air (who operated the service on behalf of AF) removing the 48 seat CR2 from their LYS base that caused the service to end. If BMIR operate LYS as their last rotation of the day after GOT and TLS then this would be more advantageous to travelers, this of course would be too simple and BMIR have probably planned LYS for a midday departure
, we will have to wait and see when the schedule comes out on the 5th of Feb.
The Flybe flight will most likely carry an AF flight code.
Daza