I just finished watching the 1840 storyline last night, and am definitely among the confused. The way it looks to me, the Collinwood to which Barnabas, Julia and Stokes returned would almost have to be a parallel time 1971.
If they changed the way 1840 had originally happened, creating a new future, wouldn't the old timeline have to still be in existence somewhere? I can't remember which cousin posted about this - it was a long time ago - but basically they thought that the 1795/6 that Victoria Winters visited had to be a different one than what Barnabas remembered, since he remembered Phyllis Wick (not Vicki) as the governess, even after Vicki's return from the past.
[Spoilery]
Similarly, since Angelique gets killed in 1840 and Roxanne does too, neither of them can have been around in the regular present day storyline. That changes the storyline so much that a present day without Cassandra/Angelique or the vampire Roxanne would have to be a parallel timeline, since they figured pretty heavily in what had come before on the show.
It's pretty mind-boggling because if Barn & co. really changed the past that much, so that the present day Collins family had no memory of Gerard (or Daphne, whom 1970 Quentin was in love with, remember?) how could the 1971 we saw be the same as the one they left? It would be so altered, a viewer would need a score card to keep up.
In this "new" 1971 Collinwood, what happened with Dr. Lang and Adam in 1968? Who knows? Angelique wasn't there to affect that. Is Tom Jennings still alive? He must be, there was no vampire Angelique. What about the Leviathans? Angelique was a major help in defeating them. Is Maggie at Wyndclyffe? She shouldn't be, since it was her victimization by vampire Roxanne that finally drove her over the edge.
Really, it's just too much.
By the way, Mysterious Benefactor - you said upthread that the writers had some plans for what they'd do with "present day" Collinwood after they'd finished with PT1841. Do you know what those plans were?