Ah, so F.Rogue and F.Lucy were from different timelines, well that explains a few holes . So currently we are on the 3rd timeline, for now it's unknown to where it will lead to, but it might revert to the original.

The 1st timeline:
- Acnologia returns and rules the world,
- 7 years later Rogue comes up with a plan and goes into past.

The 2nd timeline:
- F.Rogue comes from the 1st timeline and unleashes the 10 000 Dragons, being unable to govern all of them, they rule the world form now on,
- Levi writes her diary/message,
- Lucy survives and goes into past to change their future.

The 3rd current timeline:
- F.Rogue comes from the 1st timeline with a plan to unleash 10 000 Dragons,
- F.Lucy comes from the 2nd timeline in order to stop the 10 000 Dragons,
- it results with unleashing only 7 Dragons, while stopping the rest from coming (only F.Rogue stays alive, for now).