EASA will have the power to stop national licenses and ratings. This is what the UK signed up for, and if you don't like it, it's too late.
Whether they will use this is debatable. IMV there is no chance of them blocking it until there is a similarly accessible replacement. To do so would look terrible on the safety front - forcing a few thousand UK pilots to scud run and to do dodgy VFR approaches.
As to when a replacement will come, that's been done to death here recently. I think it's fair to say nobody really knows.
But I reckon that when it does come, previous instrument training will count towards any minimum flying time requirement.
If I was after IFR capability now, I would absolutely definitely not hang around waiting for some "new IR". I would just get on with it. Any kind of instrument rating is seriously hard work, and having say 50-100 hours under under the IMCR privileges is going to make it far easier than doing it from scratch as a pure VFR pilot. The IMCR is really useful for getting about the UK. The full IR is really for European IFR touring (it's great for that) but to do that you need to have an aircraft access deal suitable for taking it away for decent periods, etc.
If you want to fly IFR for real, instrument training will never be wasted. The only thing which is a bit wasteful is training in a plane that's very different from the one you will eventually be flying. Training in a really crappy C152 with crap avionics is not going to be helpful for flying IFR in something modern. Currency on type is what matters.