I am just going by what's in the 2.0 Roadmap. All story content from 1.19 to 2.0 is exclusive and it will be erased. No one is refuting that. I'm talking about the stuff BEFORE that. The original quest-line that was here at launch. No one can provide me with proof saying that it will be taken out, and to me it makes more sense for it to still be there, since it's the main plot of the game.
No one is saying the plot of these quests shouldn't be presented to players in 2.0.

But the way SUE events are playing out, they incorporate the old story and fill in blanks.

The whole thing can be explained in a cinematic similar to the Battle of Tavnazia in XI. "The Empire showed up in Eorzea. Meddled with the Aether and Primals. Battles were fought. Things went boom. Calamity occured."

In 2.0, the Empire will already be here in Eorzea. Giving way to a new main scenario built on the foundation laid by the old main scenario. It's not like players must experience those quests to understand the situation. And not every detail needs to be explained up front.

Hell, unless you did a high rank San d'Oria mission in XI, you missed out on a huge reveal about the events shown in the opening cinematic.

I just don't get why you think these quests absolutely need to be in 2.0. They've been absorbed into the one-time event. The conflict between Eorzea and the Empire can and will continue after 2.0, but for all intents and purposes they're likely going to cause the calamity. It'll just be really awkward from a story telling standpoint to have a player do quests about how "the Empire is coming" when in 2.0 they'll already be here and have royally screwed up everything. It's just common sense.