All grayed out achievements have had their points deducted from the total. and as vaulk described, it does seem that you can be doing something else, like a monster trophy, you get that achievement? and immediately, something else is gonel to bump your total back down again.
Like taking two steps forward, three steps back.
So you can not even just avoid dragonhold/scalecaller content and be fine. Any achievement you get anywhere else will just start removing others from your total.
Is anybody from ZOS going to let us know if they are still working on this, if progress is completely lost, and give us a timetable for a fix?