Steps to reproduce:

1- Create a nether portal and enter in the dimension.

2- Return to the overworld, or exit world.

3- Remove all files in DIM-1\region (world folder)

4- Enter through the nether portal again

5- See as the nether is re-created, but not the portal.

Workaround: You must create a portal inside nether, to connect it to the overworld portal and escape from the dimension.