Show me exactly where it says that the old church timeline has been dug up. What I've seen indicates that everything Arnold had a hand in still exists. Unless it outright broke. A bunch of legacy hosts are still in commission. The entirety of their initially story was simply buried. Not destroyed.
Also you still didn't explain why Delores has a flashback to the Man in Black while in a supposedly early timeline. Her memory of the Man in Black encounter should be like 5 days max from current time. Yet the multiple timeline people are insisting Billy is MIB -30years. So how does Billy's Delores have a memory that is supposed to be from 30 years in the future? Simple. Billy is not the MIB and there is only one timeline.
If William is the MIB, he's only been the MIB for a year at most, not 30 years like most people originally thought. So if William is the MIB, he hasn't been mistreating her for 30+ years, but more likely for a year, and probably only for several "vacations" at most. Also, it shows clearly in episode 2 that Ford is getting ready to dig up the town that was buried long ago. We then get the gigantic excavators that are digging everything up, and in this last episode we get corporate girl clearly stating that Ford has dug up (not is digging up, which is present tense, but has dug up, which is past tense) a town in the far end of the park.
With what we now know about the MIB, and how he discovered the maze, I'm guessing that he is raping/harming Dolores (and by the way, it's Dolores, not Delores) in the hopes of "awakening" her just like he did with Maeve. He's trying to evoke that same response in Dolores that Maeve evoked when trying to protect her daughter in the hopes of having her reach a state of self consciousness. Now, to what end I don't know, because we get clearly from the MIB that he doesn't want to leave the park again. So if he's trying to die in there, or live in there with Dolores or whatever his actual end goal is I don't know. But what we do know for sure is the following:
1. The maze isn't an actual place in the park.
2. The MIB hasn't known about the maze for 30 years, he's only known about it for a year.
3. There are definitely multiple timelines, and the one constant in all of the timelines is Dolores, whether it's with her interactions with William, the MIB, Ford, or Bernard, they can't possibly be all happening in the same timeline. It's obvious that the conversations with Bernard and Dolores were taking place in that secret basement, which Bernard didn't know existed until the last episode. So either there was an original Bernard who wasn't a host, or Bernard=Arnold, in which case, conversations between Bernard and Dolores were 30+ years ago, not the present.