User blog comment:Renkrisb/The Dragneel Brothers/@comment-26416024-20150519215248

Here is how I see it. For a long time, Natsu was E.N.D. and during this time he was evil and created Tartarus. We know he also created Curses. Eventually Igneel challenges E.N.D. to a fight to the death but is not strong enough to defeat him so Igneel resorts to somehow sealing E.N.D.'s powers and memories in the Book of E.N.D. Possibly with the help of someone else. The sealing has the same effect as Doriate's retrogression magic and makes Natsu small again.

It's after this point where it becomes more guess work. The only explanation I have is that Igneel used memory manipulation magic on Natsu to make him think his training with Igneel was recent and that actually after their training, Igneel somehow made Natsu sleep for 400 years. Though I doubt any of the other dragon slayers are demons, I think it's possible their dragons made them sleep for 400 years too which would explain why Gajeel could not pass through Freed's runes.