Call it what you want, his calculations whatever they might be, caused the weapon to be built. We're supposed to believe that in the end he decided not to finish those calculations after all. But why would he do that since he had no memory of another time line?
As for the episode, it's quite obvious that the writers themselves didn't understand it themselves as it is filled with plot holes and contradictions.
For instance, they can't decide if the ship is moving forward in time or if it's stationary timewise. Annorax says that they've been wandering around for two hundred years, yet he still expects his wife to reappear and that suggests that the ship is stationary via a vis the normal time. But then you have his assistant that says that for a hundred years he's been celebrating the birthdays of the dead and that says that the ship is moving forward in time. So which one is it? Besides it they were coming back to the same time period again and again as they seem to imply (sometimes) then Voyager wouldn't hard to find as it wouldn't MOVE!!!
This is just to show you how incoherent the whole thing is. And that's a characteristic of most voyager episodes, the more you think about them the less sense they make.