Based on the ways in which they wrote the show, I've surmised through the years that the DS writers didn't look at the concept of time in the same way that, say, science fiction writers do or a majority of writers might have. They pretty much viewed the storylines in terms of the points in time when they took place on the show, as opposed to their actual chronological time. Even though in real time 1840 obviously took place before 1897, the 1840 storyline took place after the 1897 storyline on the show, and the 1840 events took place after Barnabas' trip to 1897. So, to the witers' minds, anything that happened in the 1840 storyline didn't invalidate anything that we had seen in 1897 because Barnabas had travelled to 1897 before he'd travelled to 1840 - 1897 took place before 1840 in the show's and Barnabas' own timeline - and thus any changes that Barnabas & Co. made to 1840 hadn't yet taken place when Barnabas had been in 1897. Yes, that creates all sorts of paradoxes, not to mention it conflicts with a logical view of time - but there you have it. But then, that's hardly the only unique take on the concept of time in the DS universe as it's endlessly fascinating how changed events in the past had been able to change outcomes in the future like David's death due to Quentin's haunting, but they never actually changed the fact that events like the haunting had taken place because several characters still remembered. It's not so much the writers didn't expect the audience to remember - it's that they expected the audience to accept and to go with the concept of time in the same ways that they did. DS is quite simply a show with many of its own unique rules.