If you have recently switched to vanilla Minecraft from Spigot/Paper/CraftBukkit/etc. you may have noticed that your Nether and End worlds seem to have gone *poof*... Your worlds have NOT vanished! We can actually fix things right up for you and gets things back to normal.
To restore Nether/End after a Spigot/Paper/CraftBukkit to vanilla switch:
Stop your server.
Connect to your server through FTP. See this guide for help.
Once connected, open your world folder from which the Nether/End seem to be missing.
Delete the folders "DIM-1" and "DIM1".
Double-click the two dots at the top of the folder to return to your server's root directory.
For the Nether, locate the "world_nether" file ("world" will be your world's name) and open it.
There will be a "DIM-1" folder inside the "world_nether" folder. Drag and drop this folder to the double dots so it will be moved to your root directory.
For the End, locate the "world_the_end" file ("world" will be your world's name) and open it.
There will be a "DIM1" folder inside the "world_the_end" folder. Drag and drop this folder to the double dots so it will be moved to your root directory.
Once both "DIM-1" and "DIM1" folders are moved from the old world folders to your root directory, move then again, this time to your world folder.
Start your server.
Connect to be sure the Nether/End worlds have been restored appropriately.
What if I switched from vanilla to Spigot/Paper/CraftBukkit and my Nether/End worlds are gone?
These server types should actually convert your Nether and End worlds automatically from vanilla, however, it's possible that old Spigot/CraftBukkit Nether and End world folders may be taking over. This may happen if you've used these server types in the past, switched to vanilla, and you're now switching back again. In this case, try going in and looking for duplicate "world_nether" and "world_the_end" folders and deleting/renaming ones you don't want.