I have defeated the dragon which spawned the end city portal. I was able to use that portal 3 different times. However, now when I throw the pearl through it will just spawn me back on the main island. I've tried logging off the world and reloading and it still won't work.
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I was sitting on the main island where the dragon spawns. The end city portal was off to the side. I tiled up next to it and threw pearl in. It teleports me back down to the main island next to where the dragon spawns in the completely different direction than where the pearl was thrown. As I said, I’ve entered that same end city portal three different times without an issue.

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before you threw the pearl were you at the End Islands?