DM: HOO boy... How's everybody doing in here?
Fluttershy: Doing fine...
Applejack: How's the, uh, "plan" comin' along? He throw you any curveballs yet?
DM: I won't share any specifics, but suffice to say I don't think we're catastrophically off the rails yet. Anyway, what do you all want to do next?
Twilight Sparkle: Since Discord is basically on the run and can teleport at will... I was thinking that I could return to Canterlot and look into a chaos-magic-detection spell that can reach all across Equestria.
DM: Sounds reasonable, though that may take up to an entire day to set up. What would the rest of you like to do?
Fluttershy: We'll stay in Ponyville, make sure everyone's okay...
Rainbow Dash: ...and if Discord comes back, we'll make him regret it!
DM: What if you need to communicate while you're separated? ...Oh. Right. Spike.
I haven't taken part in it much, but managing multiple sets of players with asymmetrical information across different rooms always seemed both really cool and really difficult to balance such that everyone has a good time without much downtime.
My Fallout Equestria group had a bunch of bad incidents when we couldn't communicate with each other after splitting up. As soon as we were able to, we all got radios. :3
My dad's approach to GMing when the party was split was to make notes and hand them to whoever needed them. Didn't come up often as my sister and I were the only players, so Dad had to run the rest of the party.
Betrayal at house on the hill is a great game where this happens, one player (mostly at random) gets determined to be the traitor and has special rules for how they win while the survivors get a different ruleset. It's very cool thematically and design-wise. But, unfortunately, there's a massive gap in the flow of the game where once the haunt reveals itself you have to go into different rooms and read rules and/or make plans for 20 minutes while the other players do the same. It's a massive drag on the pacing.
Well, how else are they not going to make it obvious who the traitor is by ushering everyone else into one room and one specific person into a different room?
Who is the traitor isn't kept secret in BaHotH. The traitor's goal, and/or their means of achieving that goal, is what's secret. Though usually it's not too hard to figure out. Mostly the challenge of the Haunt part of the game is getting anything done, and navigating the maze of a house, without getting killed.
I haven't played a lot so this only came up once, and we didn't bother hiding what was happening.
Our party came into a small farming town, with a noticably large number of scarecrows- imediate and obvious horror plot we all twigged onto- and found out in town that the local kids were missing. We investigate, or rather most of us do, because our cleric decides to go and get drunk and our Dragonfire Adept (me) watches him. The investigating party members decide to follow a lead and find a witch in her cottage, who had kidnaped the children, and end up in a two front fight, in the doorway to the house, the witch on one side, and her army of spellcasting scarecrows on the other, the very flamable, made of straw scarecrows. In character I am dunking our drunk cleric over and over into a water trough to sober him up, and, wondering where everyone is, ask around, only to find they went off to fight the local witch, without their area effect dps and healer. I enjoyed that in character moment when I got to go "Wait, there's a witch with an army of scarecrows and my party members went to fight them all, WITHOUT the guy who can breath fire!?". Finally I get to join in the round of combat- running towards the fight.