So, the new Joker origin movie, and the Phoenix-Joker character ostensibly exists in his own timeline. Leto is still contracted by Warner to play Joker in the mainline DCEU; he also is working on a Joker/Harley project (supposedly) with Margot Robbie.
In reality though, this is sort of like what Sony did with "Venom." They suggested the movie exists in it's own timeline, until we found out that it didn't, and they were going to hamfistedly mesh it into the Spider-Man Universe, and thus, the MCU.
My guess is that the next Leto-Joker movie will not make it out of pre-production; that audiences will very likely respond much more favorably to Phoenix's Joker; and that Pheonix will take over the role as part of a DCEU micro-reboot. That'd be my guess..