The whole thing of a paradox caused by changing history has always plagued Dark Shadows. Of course, that gets into the whole is-it-possible-to-change-history thing. For example, if one traveled back in time to land on the Titanic on April 14, 1912, and convince them to change course, would that change history? It is argued that no, it wouldn't. If one went to the past and saved the Titanic from hitting the iceberg, back in the present, there would be no recollection of her sinking, thus in the present if one traveled to the past, one could not warn them, and thus she would still hit the iceberg. Maybe there would be a temporary paradox, but then time would reset itself to what actually happened.
I look at it this way, using my own twisted imagination and attempts at understanding things on Dark Shadows. Barnabas (and later Julia) go to the past and change history. Back in the present, the whole haunting of Collinwood never happened (even though David and Amy still remember it, but just forget about that). Miss Cleo and Ezra ARE still alive, since they never came to Collinwood. However, Barnabas and Julia are somehow "protected" from not remembering the changed circumstances because of their time-traveling. But everyone else has no memory of something that never happened.
Gerard