I think thye got no choice really other than remove the markings of the EM145's. I doubt BA want them to keep the A/C in British Airways livery and doubt Flybe want to advertise BA.
Passengers are being missinformed on the CDG - CWL - BHD route. Passengers that wishing to travel CDG - BHD are not aware when they book that they are in fact going to CWL first.
Another problems where passengers have liquids and have to take all their belongings off the a/c and clear through imigration, and then go through security at CWL to then re-board the a/c. Some of them have liquids which of course then gets confiscated.