I had a world in 1.16.5 with a custom dimension in it. In 1.16.5 both the End and the custom dimension were working perfectly well, but I upgraded the world to 1.17, then to 1.17.1. I didn't check if they were working in 1.17, but I checked in 1.17.1 and both the End and the custom dimension were treated as if non-existent. The End portal was not working, and neither the End nor the custom dimension did not show up in the auto-complete for the /execute in command and could not be accessed with it.
I tried disabling and removing the data pack with the custom dimension, which did not work. Reloading the world didn't work, and restarting Minecraft didn't work either. But when I created a new world, the End did work in the new world. What happened?
Update: It appears that after upgrading a world with custom dimensions to 1.17(.1), the custom dimensions, as well as the End, disappear from the level.dat file.
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Update 2: I have determined that the problems are caused by the level.dat file, which were missing the tags for the End and the custom dimension. After adding back the tag for the End using an NBT editor (copying values from the 1.16.5 backup), the End became accessible, but after adding back the tag for the custom dimension (also copying the values from the 1.16.5 backup), both the custom dimension and the End were removed from the level.dat file.
Does MC-197860 describe your problem?
No, but similar issue. The bug appeared when the world was updated, even though no datapacks were deleted. My custom dimension was not using the default namespace either.
Update: It appears that the inaccessible dimensions in the world are missing an "entities" folder, while the accessible dimensions in the world, as well as dimensions in other 1.17 worlds, have an "entities" folder.