Yes - as I said, if you're concerned about the details of *characters* and *events*, especially in eras outside of the now official canon, there will be changes. Using language like "completely eliminated" or "irreconcilable" for everything other than the NJO era is way overstating things though.
However for the purposes of a role-playing game, things like (current) organisations, planets, species and technology are typically much more important, and for these things the Legends (i.e.: in this context RPG material, old and new) and canon are converging.
Uh, the characters and events are just as important for a roleplaying game as anything else, those events define the universe the characters exist in.
I'll certainly call things irreconcilable, because they are. In the original canon of Star Wars, Luke Skywalker re-founded the Jedi Order in 11 ABY by founding the Jedi Praxeum on Yavin IV and taking his initial class of students, who went on to become prominent figures in the galaxy. . .while in the Disney universe, Luke ran off to become a hermit and refused to train apprentices and nobody has seen or heard of a Jedi in decades. That makes a huge difference in how you would play a Jedi character in a game, for example.
If you're playing a Force Sensitive character, say, 15 years after the Battle of Endor, are you playing one of a new, rising group of Jedi studying under Luke Skywalker (or maybe Kyle Katarn) and serving the New Republic and fighting the Empire, or are you a lone renegade figure with no allies or mentor in hiding from Kylo Ren and the First Order?
Setting matters. Try taking Forgotten Realms or Dragonlance and ripping out about 95% of the chronology in both directions, saying that only a few of the most famous works are still canon, but future setting materials may re-use some old elements at time as they tell completely and utterly different stories, and that's "convergence".
You say "current" like that means a specific time. The Star Wars setting, ignoring Disney's reboot, spans ~36,000 years, from the Dawn of the Jedi series on Tython around 36,000 years before the films, to the events of the Star Wars: Legacy series 140+ years after the films. There isn't one specific time for Star Wars, it's a vast saga that can have adventures across thousands of planets and tens of thousands of years. . .Disney Wars takes place over about six decades, and a couple dozen planets.
That's the vast, overwhelming bulk of the Star Wars setting that Disney is trying to toss down the memory hole with their reboot. I can point on my wall of Star Wars RPG books to large number of RPG books that are absolutely incompatible with the Disney Wars setting: Knights of the Old Republic Campaign Guide (contradicted by the pre-history of the Republic given in the novel Tarkin), Legacy Era Campaign Guide (contradicted by the new movies), New Jedi Order Sourcebook (contradicted by the new movies), Dark Empire Sourcebook (contradicted by the new movies), Truce at Bakura Sourcebook (contradicted by Aftermath), Thrawn Trilogy Sourcebook (Contradicted by the new movies), Courtship of Princess Leia Sourcebook (contradicted by the new movies), The Jedi Academy Sourcebook (contradicted by the new movies), Strike Force: Shantipole (contradicted by Rebels).