I was using online examples to set up custom dimensions for my datapack when I suddenly lost access to the nether and end dimensions in my vanilla world. They existed inside the world file, but were inaccessible. I could not run 'execute in' for any dimension aside from overworld, and portals could not teleport me.

How to reproduce

1. Load a datapack that has a custom dimension using the default namespace
2. Open world
3. Close world
4. Delete the datapack containing the custom dimension
5. Open world

Video Example

 Depending on the resource location of the dimension, both nether and end could be gone or only one of them.

I was able to reproduce this bug multiple times, including on worlds generated in older versions like 1.15. The world does not have to be generated with the datapack–it can be added later. This process does not cause deletion of vanilla dimensions when custom dimensions use namespaces that are not 'minecraft.' This is a datapack I found online for free use, I did not create it. My client is unmodded. I also tested this in 1.16.2-rc2, at which the same bug occurred–though I was not able to mark it on here for some reason.

One last thing I noticed is that you do not even have to load the custom dimension, and the deletion of the 'dimensions' folder I did in the video is not required either for the bug to occur. Merely load the datapack in the world once, close the world, delete the datapack, and load the world again.

That is all I believe. I will try to monitor this thread if further information is needed. Thanks!