"master" files is astrophotography jargon for integrated files - "master dark" == integrated dark from dark subs, "master flat" == integrated flat from flat subs, etc.
are you using an OSC or a mono camera? PI won't merge the 3 filter images into an RGB image on its own, if that's what you are looking for. if you had subs from R, G and B filters, you'll find 3 master lights, one per filter.
i should add that "integrated" doesn't mean "RGB combined" - integrated simply means "added", in the mathematical sense.
rob