I don't know why but SE didn't change the Job storyline in 2.0.

The old Job storyline is still there but background is changed and the battle been given more mechanics.

Is there a lore reason why 5 years later the events of 1.0 Job storyline are repeating themselves in 2.0.

I can only guess that as...

New Adventurer: the Legacy players never took on the Job storyline in 1.0 so the events of 1.0 Job storyline never happened until 2.0

Legacy: Because of the Calamity not only was the memory of the Legacy player was gone but the events of the Job Storyline was reset as well. Leading to the surviving members not having any memories of performing the same events in 1.0.