A girl named Anna

The dragons spent five years training the children before they sent them into the Eclipse. They themselves didn't enter it, and instead used a technique of their own creation called the Dragon Soul technique to seal themselves within their children's bodies. This also allowed them to manipulate their memories slightly, making them believe that their parents had abandoned them. This pained the dragons, who had truly grown to feel kinship with their students, but they also knew that the children needed time to grow, and their appearance would only invite Acnologia to take them down before they were ready.

Zeref was also still busy during this time. It was all well and good that the Eclipse was being completed, but the thing needed a mechanism to open it. The mechanism Zeref chose was a special type of space magic that used unique artifacts to interact with and contract powerful beings from another dimension. This magic, known as Celestial magic, was the most powerful form of space magic, and it just happened that all twelve of the strongest artifacts used in celestial magic, the Zodiac Celestial Spirit Keys, were currently in the hands of a single woman, Anna Heartfilia.

Anna was not exactly a fan of Acnologia, as she generally wasn't a fan of randomly killing people just because they might become a threat to you, and she accepted the role. She acted as a mentor and guide in the ways of humanity to the young dragonslayers. Her lessons made sure that they would be able to adjust to the world that they were entering, but she was also convinced to simply go with them. She had a sister named Amelia Heartfilia who would keep the keys and pass them down her lineage until they were ready to reopen the door.

The Eclipse was laid down in the Land of Flowers, just a few decades after the largest battle Acnologia had waged was fought there. It had redeveloped, and a new monarchy had risen there. Zeref entrusted the Eclipse to them, and Amelia's lineage was granted special protection by them. At the appointed time, they would meet together and the dragonslayers would begin their quest.

For a time, both worlds were quiet. From 1640 ARI to 1805 ARI, the worlds simply progressed naturally. The people of the Pokémon world simply exchanged ideas and grew their knowledge, while Acnologia was quiet in Erathalia, and the Land of Flowers transformed into the capital city Crocus of the nation of Fiore, occupying just a small peninsula in the west of Ishgar.

[AN]: Ishgar is their world's name for the central continent that visually looks similar to an Italy-less Europe, with the much larger Alakitasia to the west. Similar in size to Alakitasia is Guiltina in the north, and the unknown Eastern continent lay in the East, with little to go on thanks to the Renquist Kingdom in the far east of Ishgar keeping tight-lipped about what lay there. In Fairytail the action focuses on Fiore in Ishgar and Alvarez in Alakitasia, so little is known or mentioned about other nations. The closest we get to learning about other cultures is that Bosco has legal slavery of some sort, and it is directly east of Fiore. For the purposes of this narrative, I'm going to basically treat the other countries as functionally non-existent, which is about the level of impact they have on the story.