The main theme of that episode (DS9: The Visitor) is that Jake's father was trapped in time. By freeing him, Jake caused that particular timeline to cease to exist.
JAKE SR: You see, Melanie, after the last attempt to rescue my father failed, I spent months trying to figure out what went wrong.
Eventually, I came to understand the nature of what was happening to
him. It was as if he was frozen in time at the moment of the accident,
and the link between us was like an elastic cord. Every so often the
cord would go taut enough to yank him forward into my time. But only
for a few minutes. I realised that if my motion through time came to a
stop, the cord would go slack and he'd be lost in subspace forever.
But if I could cut the cord when the link was at its strongest, while
we were together, he'd return to the moment of the accident.
Given that Jadzia died as a direct consequence of Ben's ongoing feud with Dukat, it would appear that his disappearance resulted in her not dying in season 6