See my 4 timeline theory

We know Dolores enters the church twice, once in a blue dress, and once in a cowgirl outfit. We also know she dies in the river in a cowgirl outfit. We also know the church is buried.

I propose:

Timeline 1 (Arnold's, earliest, prior to park incident): Church is whole and full of hosts, presumably suffering from cognitive dissonance. Dolores (blue dress) goes down the confession booth to speak with Arnold

Timeline 2 (William's, closest timeline to the park incident): Church is presumably whole. Dolores (cowgirl) travels with William, gets stabbed and dies in the river

Timeline 3 (Dolores's, most recent timeline, 40 years after park incident): Church is whole, Dolores (cowgirl) finds church empty (she's alone), realizes Arnold's dead. *See note below.

Timeline 4 (Ford's, when MIB guts Maeve, probably like 39 years after park incident): Church is buried and burnt. The Maeve incident causes Ford to unearth the church for his new narrative.

*We know there are two Dolores (cowgirl outfit, timelines 2 and 3) timelines, one where she travels with William, and one where she travels alone. Look in episode 5 in the train scene with Lawrence, after William and Lawrence sit down with a drink, Dolores tells Arnold that 'She's coming' and as the scene pulls away, the train cart is empty. She completes the train ride twice, once with William, once alone. Probably a third time in the blue dress. A second argument for this is in episode 9, where cowgirl Dolores is stabbed by Logan, but also not stabbed.