When fighting a respawned Enderdragon, it will often fly into an already-generated end gate. This causes the dragon to glitch out. The health bar will still be there, and the dragon will be flapping next to the end gate, but the dragon will be un-damageable. A new end gate will spawn as if the dragon was killed.

This happened to me three times in a row while trying to get the "The End." achievement from one of my imported worlds.