Crossing of Time Loops

I had to make a backup of a very well developed world. I had just beaten the ender dragon in the original world but something went wrong (don't worry about that issue, it was my fault) so I made a backup. This backup was made 17 days before I had beaten the dragon and gotten the elytra.

I'm back at the end again (which should be for the first time in that backup world) and I got all the first time achievements for getting to the end. But everything that I did when I first fought the dragon is there. All the end crystals are gone and the dragon egg is gone. The portal back home is already active and the End City has already been raided.

Everything that I got at the end (dragon egg, dragon head, elytra) are all gone so I can't get them again. The backup was made about 17 days before I had beaten the ender dragon so I don't know how this could all be there. Please fix it. 

Username: Nox_ES73, Seed:495368034