With the introduction of this time-travel business, I think it's safe to say that Nastu, Gajeel, and Wendy were originally from 400 years ago and traveled through time without knowing, thinking that the dragons disappeared when it was actually them that disappeared. Also according to the Fairy Tail Battle Royale thing from quite a while ago, Gajeel and Natsu are both over 80 years old. So either the 3 dragon slayers were frozen in time for 400 years, or they traveled through time and the runes considered them above 80 years old because the runes judged age by birth date minus present date and not because of how long they lived.