“So what’s happening with Sombra and the Crystal Empire arc if we’re skipping forward to Magical Mystery Cure?” I see you asking. Perfectly reasonable question. I’m usually loathe to lock down canon outside the contents of the pages, but in this case it’ll be a while before it comes up, so here’s my thought process.
We’re not doing Sombra’s first appearance because 1) it’d be weird to have Shining and Cadance guest twice in a row when it was meant to be a one-time opportunity; 2) the lessons they gained from Shining and Cadance directly helped the group gear up for Discord, and I don’t want to lose that momentum; 3) Shining and Cadance have their own pony game group, so the discovery and salvation of the Crystal Empire will happen for them “off-screen” (in a way where they get to do the action and save the day and not just be supporting characters twice in a row); and 4) there’s another opportunity down the line for the Mane Six and Sombra to face off that fits with all this.
Hope that clears things up!
Twilight Sparkle: We’ve contained Discord’s influence to Ponyville… If we just go in without using the Elements, we get sent to some random alternate-dimension Ponyville. Which lets us deal with his power without directly confronting him… Weird as it sounds, that might be the perfect place for me and my friends to find the power within ourselves before confronting Discord.
Princess Celestia: That is… an exceedingly dangerous plan. Do you believe it is worth the risk?
Twilight Sparkle: Yes. Because Discord’s not gonna make it easy. He’ll do anything and everything to win, and we need to be prepared for that. Do we have your blessing?
DM: Celestia thinks for a long, silent moment. And then she says–
Princess Celestia (Applejack): “Y’all are crazy, Ah’m outta here.”
Rainbow Dash: Heh heh heh!
DM: Aha, no, no, c’mon… Well… I’d be lying if I said she’d never occasionally thought something like that.