I've recently upgraded my 1.19.4 world to 1.20.1. I've already got 2 existing gateways in the end. After updating my world, I killed ender dragon once again but it didn't generate a new gateway. The game kinda re-regenerate my existing gateway and it arrives the same point.
NOTE:
This happened twice but in the first time I was using iris shaders and the issue flagged as invalid. This time I've replicate the same steps with plain vanilla Minecraft, no mods.
To duplicate the issue, you should have a world played in 1.19.4 and has at least one gateway generated in the end after beating ender dragon. Create a platform around the gateway so you can see the disappearing blocks when the bug happens. After close the game and update your world to 1.20.1 with minecraft launcher. Then re-spawn and kill the ender dragon to generate another gateway.
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I can't reproduce this. What I did was:
Create a world in 1.19.4
Defeat the ender dragon, spawning a gateway
Went through the gateway and marked the area
Updated the world to 1.20.1
Respawned and defeated the ender dragon again
A second, additional gateway was created that took me to a different area
Please let me know if I understood your problem incorrectly
I think after the update, the existing gateways just resets itself. After re-generating my existing gateways, I could generate a new gateway.