Yes, really.
First of all, there was no Universe A or B. Zedd's actions completely wiped everything that happened away, resulting in completely different events up until his point in time. He didn't jump to some alternate universe. There weren't two different universes existing simultaneously. He accidently changed time, plain and simple, and didn't realize how important Kara's role was until he did so. That, too, was one of the big reveals as part of the seasonal arc.
Second, as previously stated, we also learned that the Keeper is immune to changes in the timeline. That even when Zeddicus (even if unintentionally) unleashes amazingly powerful magicks, the Keeper would still be a very real threat... and one that they wouldn't be prepared for if he did try to tinker with the timeline.
Third, the seasonal arc continued despite the changes. The Keeper's plan simply changed to adjust to it, and the heroes, would-be heroes, and never-were heroes all played a part in those events.
Your insistence on comparing it to other shows, and being oblivious to the fact that it's very much a part of the seasonal arc, is a failing on your part, not the show's.
