User blog comment:FairyRaven/Fairy Tail Chapter 337: The Golden Plains, Review and Commentary/@comment-4933386-20130628120559/@comment-4829046-20130628124020

Let me explain. Now listen and listen well Jk =P

In F-Lucy's future the gates opened and out came 10,000 Dragons though this is very unclear. These 10,000 Dragons destroyed humanity and took over, forcing Levi to hide and write that letter. Sometime before that Lucy had awakened and found that all her friends were dead, and so she went back in time. This bit is directly from the story. Here comes the kicker

Now, say that the gates were destroyed, and the Dragons didn't appear. That WILL NOT STOP ACNOLOGIA FROM DESTROYING EVERYTHING!!!!, it will only result in F-Rogue's timeline except the F-Rogue will have no way of time-traveling.

Even if F-Lucy's timeline was fixed and everything was peachy again and Lucy never died due to the gate not being there, Acnologia will still be there. He will destroy them anyway. So the only conclusion is that they all died and went to heaven.