They wont remove the dugeons or related achievments.

All the current grand company progression quests will be gone as they are all garlean invasion/dalamud/7th umbral era related.

The grand company side missions will stay as there not related to the impending doom.

If you noticed we dont actualy rank up for completing GC quests, to rank up you need to spend seals which i guess they had to do if they were to remove a bunch of GC quests and start a new GC story in 2.0.