Nobody is saying that the events of Judgement Day changed Alpha's past, only that it might have changed Dredd's future and sent it off into a parallel timeline. That needn't prevent Dredd and Alpha from meeting again in stories like By Private Contract. (Well maybe it should, but comics.)
Yeah. I banged on about this at some length in a post I can't be arsed to google up, but, specifically supported by the way that time travel/paradoxes seem to work in the Dredd universe, it's entirely possible for Dredd's world to exist as part of Alpha's past, without Alpha's world having to exist as Dredd's definitive future. The timelines can diverge at any point after any of their currently documented meetings without implications for either timeline. In fact, Dredd could visit Alpha's future, but assuming a divergent timeline, he would need both
time travel and a D-Jump to do it.
Al Ewing has already introduced the idea that Justice Dept has a dossier on what little they know about Alpha's future. It's possible that there is a plan being hatched (in-fictional-universe) somewhere to ensure
that the timelines diverge, since ending up in Alpha's future requires the complete end of the Judges and, by implication, the Mega-Cities.