I'm not sure if you would still like an answer to this issue, but I had the same issue as you & tried to fix it in the same ways. So I figured out the issue & how to solve it!
What I did was dig into the NBT files of the world. In doing so, I saw that the End & Nether dimensions were missing from level.dat. That explains why even with the DIM files, the game thought that the dimensions didn't exist. This also explains why other worlds dimensions worked fine.
So, here's how I fixed it:
(edit: make sure to not be in the original Minecraft world while doing this.)
I copied the world seed & created a new world with it. I'm not sure if having the same seed is necessary, but I wasn't going to take the chance.
Now, open NBT explorer twice, to have 2 separate windows of it open. Click the "Open folder" button in both of them. Now, in one window, select your original world folder, & in the other window, select the new world with the same seed (make sure to click okay when ONLY the world folder is SELECTED). In both of these windows, travel down this path:
+ level.dat > +data +WorldGenSettings > +dimensions
(level.dat_old is irrelevant, so don't worry about it).
here, you should see every dimension in the world. Now, in the window that has the new world with the same seed, select the dimensions missing from your main world (one at a time) & copy it (you don't need to click the + next to the dimensions, because you only need to copy the whole thing, not any individual subfolders inside it.). Ctrl+c, or the copy button at the top, whichever works. Then paste it into the 'dimensions' subfile. (Make sure you paste the dimension while ONLY the dimension subfile is selected, otherwise it could end up somewhere it shouldn't be. You'll know you did it right when it's in the same place as all the other dimensions).
Once you finish, make absolute certain that you click the save button at the top of the window, otherwise nothing will change. Since you got what you needed from the new world, you can just delete that once you confirm it works.
I hope this helps you, & anyone looking for the answer in the future!
