User blog comment:Stone Roger/Natsu and Zeref have somekind of relation?/@comment-89.114.120.9-20130615204803/@comment-7418318-20130617101145

If the dragon parents really were sucked into Edolas in X777, then they would have been returned to Earthland when Mystogan removed all traces of magic from Edolas and would have returned together with Natsu & Co.

With everyone (Exceed and Humans) returning at more of less the same place, I think someone would have noticed three grown Dragons.

As for how Zeref could throw the world into chaos I have two possible theories.

1) Zeref is somehow responsible for sparking off the Dragon Civil war and it was through this action that the world was thrown into chaos.

2) "400 years ago" refers to a period of time rather than an exact date, maybe even spanning several decades. Zeref might only have thrown the world into chaos, after the Dragon Civil War (which ended with the Dragons almost being wiped out and the survivors most likely hiding from Acnalogia) was already over.