They are part of Tui. Have been officially since 2 SEP this year and therefore have only consolidated their programme. Ironic how you still view them as a seperate company!
As far as im aware, the airlines will still be operating under their own names for a while yet, just under the TOM AOC.
Whereas MYT/TCX are currently doing that as of this month and will gradually phase out the MYT brand over coming months. (correct me if im wrong - its all very confusing!)
As far as CWL goes, Currently FCA operate TFS/CWL/TFS W pattern with EXT based a/c during winter, there wont be an FCA a/c at CWL as of next summer.
FCA will only exist at CWL as a tour operator. And Vice Versa at BRS.
Therefore FCA have effectively pulled out of CWL in favour of BRS and Vice Versa.
However they have as you say consolidated their programme as TOM are taking over the majority of the FCA flights with their own 757.
It has been talked about that in the long term it will all become one brand (TUIFly), but i dont think anything has been confirmed, as there was talk of TOM concentrating on S/M Haul and FCA concentrating on having such a strong Long Haul brand.