I'm sorry, but you've been provided with misinformation. The content we are talking about are the main storyline missions that you get from the Order of the Twelve and Ashcroft Consortium, etc. They never said we could only do it once, they said it will be available after 2.0 and they will build on it.

Think of it like a normal RPG from the PS1 era. The main storyline missions are like Disc 1. After 2.0 they will be adding Disc 2. They wouldn't try and sell you a copy of Final Fantasy VIII with the first disc missing! Of course we'll still be able to do the main storyline quests. Would you play a game of FFXI with all the expansion packs, but without the original content? (The Shadow Lord fight, etc.)
I still have yet to see where they said it will remain.

A lot of the main scenario is based on current geography. Given that the maps are going to be completely designed the maps, they'd have to redo the whole scenario. Otherwise it'll take place in locations that don't exist anymore. Plus, the new map concepts show the empire occupying land on the same map as the Immortal Flames. The entire current main scenario would be a "no shit" moment when it deals with the Empire as a looming threat.

I made a thread about this a while back and one of the localization team members responded to say the current scenario and all it entails will come back as the world reacts to more current events.


(Tread carefully, spoilers ahead)

Here's my guess at the story line and how it will lead up to the map redesign and 2.0: The main scenario establishes that the Empire is here and wiling to use all it's power to get what it wants. The Seventh Umbral Era events show the Enpire is getting more aggressive and the Aether is becoming unstable. They'll tie together in 1.22 and 1.23 with the Empire and Legatus battles where we'll end with a severe cliff hanger. To start 2.0, the Empire will have caused the Aether to go completely unstable resulting in the drastic changes in the land with which we are so familiar.

I suggest anyone who thinks the main scenario and the Seventh Umbral Era events are separate to go back and read the full dialog for the quest Ceruleum Shock. It ties the two together. Where the main scenario ends with us seeing first hand that the Empire has taken a significant interest in Mor Dhona, the SUE events are explaining that there is more to it than just the dragon and the ship.

That's why it'd be silly to have the current main scenario in 2.0, it's part of SUE even if not originally intended that way.