no - stack each filter, after having registered all subs to the same subexposure, to the same subexposure (so meaning pick one sub, L,R,G,B or whatever, as the registration reference for all of the different filter subs).
then do whatever you want to do to the 3 or 4 master images - deconvolution, linear noise reduction, etc.
then combine to RGB and process. process the L separately. then do LRGB combine, effectively replacing the L component of the RGB image with the processed L master.
rob