the "older" way to do this is to prepare your master flats separately by loading the flat darks and the flat subs together with a dummy light and running BPP. then you get a master flat which you can subsequently use in another run of BPP.
having said that, i see that in BPP 1.51 under the "flats" tab there is a checkbox that says "calibrate with flat darks only". if you load flat subs that match the duration of the flats, BPP should identify those darks as belonging to the flats and use the flat darks instead of trying to scale darks of a different length. i don't know when this feature appeared... but i think it would do what you are looking for.