I would suggest progressing as far as you can in the Grand Company storylines. These will be significantly changed/removed.

I would also suggest progressing as far as you can in the main storyline quest string (that begins with when you create your character). I doubt they will REMOVE any 'main' storyline quests, but it would be nice to be 'up to date' on what's happening as it happens.

They might also remove/change some smaller quests for the sake of continuity, but I wouldn't really worry about these.