They didn't undo what happened in the year 3000 with the fossilized dog, but Fry went back in time and lived with Seymour during the time period where he was supposedly waiting in vain for Fry to return. So they wiped out the part of the story that made it so sad. Or at least that's how I remember it. Maybe I'm getting something wrong.
Maybe I should rewatch the later seasons again but I really thought most of it was pretty weak. I'm pretty surprised anyone would like them more than any of the original seasons.