By the beginning of Extermination, it became abundantly clear that the team's continued presence in the present-day would have disastrous effects on the timeline. In Extermination #1, an adult version of Cable, the time-traveling X-Man, laid out the case for keeping the X-Men in the present while fighting Kid Cable, a younger version of himself who was more focused on preserving history.
The adult Cable said that the original X-Men needed to see what they became so they could go back in time and grow into something better. While there is some logic to that argument, Kid Cable said that it wasn't worth the risk of changing history and settled the argument by killing his older self.
After undoing the team's only major physical transformation by forcibly giving Angel a new set of feathered wings, Kid Cable ultimately proved his point by successfully taking the team back to the moment they left for the future. Using her telepathic abilities, Jean wiped her and her teammate's minds and essentially put their repressed memories in a psychic time capsule that wouldn't open until Extermination.
Thus, after the mind-wipe, Beast continued his rant about quitting the X-Men and the timeline has apparently gone back to normal.
As those teenage X-Men grew into adulthood, X-Men history proceeded as it always has. As soon as Kid Cable sent the original X-Men back into the past, the adult X-Men all regained their memories of their experiences in the future. Since the young Jean figured out how to defeat Extermination's villains, the adult Jean suddenly remembered how to quickly defeat those two psychic foes.
In the final moments of Extermination, the adult Jean, Angel, Beast and Iceman all got together to discuss how odd it felt having all of their old memories unlocked again. Although it's not explicitly stated, Cyclops, who was revealed to be alive on the last page of Extermination #5, presumably went through a similar experience.
Since the adult versions of the original X-Men remember their youthful adventures in the present day, the last five years of storytelling and character development hasn't been totally negated. Now, the adult Beast can easily draw upon the mystical knowledge his teenage counterpart gained in X-Men Blue, for instance.
Still, Extermination ultimately took characters that had been fully fleshed out with modern storytelling sensibilities and devolved them into the more one-dimensional teenage X-Men of the relatively simplistic Silver Age.
While that decision might not sit well with fans who grew to love the teenage X-Men in their modern day adventures, the time-displaced X-Men's saga was always going to end this way. But given some of the X-Men's apparent unease with their newfound memories, future stories may very well echo these concerns and explore the friction between these X-Men's memories of the past and present.
While the past five years of X-Men stories have been focused on the past, the X-Men can finally start focusing on the future that they've been fighting to protect all along.