They could have it be that its riding the opposite horse for your version?
You can still access that other horse through group missions without interacting with the other version, but even beyond that I think that anything you can access through snacks is off the table (barring maybe a special occasion, like maybe we get a Shiny Rayquaza raid to tie into the anime or something) so I don't think they'll both doing anything with the horses again.
I also think they'd still have to have both raids available, and I think the way the game works is it just checks "did you catch something in this specific raid" so unless there's a check that would basically exist only for this scenario we're still in a double up situation.
Regardless, we're probably a ways away from whatever plan they may/may not have for Calyrex. Assuming they do indeed want to hit all the remainder as raids there's still Giratina, the lake trio, all the regi, the forces of nature, the wolves, eternatus, Heatran, Cresselia (feels like Darkrai should have been tied to THAT instead....), probably the Galarian birds...there's also technically Cosmog I guess. I dunno if they bother even giving that away.
honestly listing them all out I don't think we're going to get all of these lol.
