There's a ton of X-stuff happening in Secret Wars, with a number of classic settings/universes being incorporated into it. So I don't think whatever comes out of it for X-stuff will mess too much with the X-Men movie universe. Even if Quicksilver and Scarlet Witch are retconned for now to be Inhumans or just something else not X-related, they've been all over the map for so much of the past that I imagine they can still play in the MCU and X-Men movie-verse going forward.
FF I'm less sure of. The movie seems to be going way off on its own path for its reboot, and its possible comics creative people just aren't a fan and want to distance themselves from this movie. Then again, the FF are figuring prominently in the events leading up to Secret Wars, so who knows?
With 50+ years of back story so far, I can't imagine both the FF and X-Men continuing in some recognizable fashion after this event. We'll see!
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