To my understanding I still only take one set of dark frames, and in fact can continue to use my old dark frames. During dark frames the shutter is closed so filter or no filter it doesn't matter.
Flat frames I would need to re-do because the image train has changed so the FOV etc has changed.
But ... I won't do that for now.. currently have my back neighbour machining up a pice of equipment that's going to change my image train length yet again, so will wait.... (a 2" tube to put my focal reducer optics inside).
Roger.