Thinking about it, depending on how the movie is plotted, having Cyclops return would work just fine while not completely disregarding X3.
This is coming from someone who vaguely knows the DOFP story in the sense that I know the basic story but never actually read it…
If the movie were to open with a time traveler assassinating the prominent figure, that alone right off the bat creates the alternate timeline in which the events in X3 (and possibly X2) happened differently?
So technically, X3 could still exist while having Cyclops and the rest of the X-team live in this now altered universe.
Then again i'm going by BTTF logic.