I was under the impression that it was a similar situation to already crafted versions of dyed items with different stats, where the existing ones would stay for now, but no *new* ones can be created. So when you're mining or whatever, any newly generated HQ materials will be the new +1 version and once you use up the old stuff its gone for good. Not the most efficient way of doing it, but i'm fairly certain thats how it works now, correct me if i'm wrong.