I saw a theory that Caleb is inhabiting Charlotte's body, and there is more timeline fuckery going on this season. I'm having a hard time believing that, since all the events involving Caleb would have to occur before any of the Dolores / Charlotte scenes. I think the chronological order would be something like:
1. Dolores-as-Charlotte (Charlores) escapes the park with 5 pearls
2. Charlores masquerades as Charlotte at some of the Delos meetings.
3. Charlores builds a host body for someone (unknown Helper, possibly the scotish guy)
4. They build a Delores body and put her control unit inside it.
5. All of Dolores / Liam and Dolores / Caleb interactions occur.
6. Dolores refurbishes the Charlotte body and puts Caleb in it. Since he already appears to have some cybernetics (fixing brain damage from that time he alluded to getting shot in the head) maybe he already has something equivalent to a pearl in his head.
7. All the scenes of Charlotte interacting with her ex, her son, Serac, etc.
My problem with that is step 5. Dolores spent a good chunk of time cozying up to Liam, and for the duration of that time there was no one in Charlotte's body. How does one explain her extended absence from Delos during this time, a long vacation?
I hope not, because "some or all of what you've seen was just a simulation" is such lazy writing. It's a cop-out to cover over inconsistencies and plot holes.