So let me explain my situation. I had a long break from Minecraft and skipped version 1.9 to 1.11. So my old Survival world jumped straight from 1.8.9 to 1.12.2. I have a big issue in this world now. It seems like the old end main island does not reset to the new island that was added in 1.9. The outer end islands generate fine, the area was not loaded before. But yeah, the main island is still as it was in 1.8 with the old obsidian towers, the old portal and the dragon is also not able to respawn. Is there any fix for this issue so I can get the new end main island? Going back to older version is not an option because this would cause corruption in my world.
Thanks for your answers guys. The deleting chunks option would actually work because I have not really build anything on the main island so far. But I have found a better solution now. If a bedrock block from the old portal gets removed then the game does not notice it as a complete structure anymore. After that you can place an obsidian block with an ender crystal on top a few blocks away from x=0, z=0 and it will spawn the new portal. With this portal the dragon can now be respawned + all the obsidian towers.
(Solution was found in the 8th and 9th episode of Ilmangos SciCraft series.)