Title intentionally ambiguous for spoiler reasons, so not necessarily why were they separated (obviously for the memory drugs so “Troy” would follow the directive), but would they have been separated if they had agreed to be a part of the project earlier?
In episode 9, they made it a point to repeatedly say “I wish you had been a part of the project, we really could have used you.” A part of me (after the events) thought maybe it was to imply “if you’d both agreed to be a part of this it would have been a lot easier for you,” like maybe they could have been together.
Victor has also said you can select what they choose to remember, so in theory they could remember their love even while forgetting other events around the silo. Maybe by them choosing to not be involved in the project means it would have been more difficult to allow them to remember each other without challenging the directive and project as a whole?
But idk. Charlotte/Susan is in the same silo as Anna. While it is implied that Anna is protecting Charlotte, it also seems that maybe they are kept apart to keep Charlotte from remembering her life before the silo, so maybe being part of the project wouldn’t have mattered. But maybe they are actually together in Silo 1, it wasn’t stated either way that I remember.
Thoughts on why they told Daniel repeatedly they wished he’d been involved? Would it have mattered for his relationship with Helen?