eeyup, or at least it had been a very long time between the two events. The invasions from Black Marsh to Morrowind happened just before or during the very beginning of Titus Mede I's rule (very early in the beginning of the era), while The Great War happened during Titus Mede II's rule, which was 35 (30?) years before Skyrim.
With The Red Year, it was a time to strike the dunmer, not have it happen and do nothing. Plus, the argonians are not buddy buddies with the Thalmor, as they did kick them out after they took over portions of Morrowind that had been fought over for a very long time.