Yup. Don't ask me how or why The CW did it, but straight out of the gate, despite "Crisis on Earth-X" being initially billed as a backdoor debut of The Ray in the Arrowverse, "Crisis on Earth-X" made the soon-to-debut Freedom Fighters: The Ray impossible and incompatible with the Arrowverse.
My suspicion is that current events in US politics provoked the Arrowverse producers to do a Nazi-themed crossover earlier than they otherwise might have (since I think the original idea was to have FF:TR come out before the Ray's live-action appearance, as with Vixen), so they had to go ahead with their version of Earth-X and the Ray before the animators had time to complete their version, but too late in the game for the animators to substantially change their version. So the changes they made to the story to fit the crossover's needs (which had to take priority, both because FF:TR wasn't out yet and because the principal work with the larger audience always takes precedence) couldn't be reflected in the webseries, and thus it ended up as a canon orphan. Although that does not explain Mr. Terrific flying.
The problem is, if the animated series had only taken place on a single Earth, we could just assume it was another parallel world that was close but not identical to Earth-One. But since it was a multiverse-crossing story that explicitly identified its settings as Earth-One and Earth-X, that makes it irreconcilable.
Of course,
Vixen has a couple of continuity issues with the Arrowverse too. It shows the Anansi totem as a flexible string of beads and teeth rather than a rigid metal carving, and it shows it as binding itself to the user so it can't be removed. It also shows Cisco naming Vixen, when in LoT the name was inherited from her grandmother. The element totems also look different in the two shows, and Kuasa has an African accent in
Vixen and an American one in LoT. But those are minor continuity glitches, on a par with the discrepancies that sometimes exist between the live-action shows (like Jax needing parallel Earths explained to him in
Crisis even though he'd met Supergirl the year before).
Then there's
Constantine: City of Demons, which we were led to believe would be a sequel of sorts to the NBC show, but turned out to be a complete reboot with more comics-faithful versions of characters seen in the show, and is apparently meant to be in continuity with the
Justice League Dark animated movie instead.
