Knowledgebase

The directory that Minecraft reads the Nether and End from differs between different server versions.

Vanilla and Forge servers will read them from the /<world name>/DIM-1/ and /<world name>/DIM1/ folders for the Nether and End respectively, whereas CraftBukkit and Spigot servers will read them from the /<worldname>_nether/ and /<worldname>_the_end/ folders.
If you switch from Vanilla to CraftBukkit for example, the Nether and End will have 'reset' due to them being loaded from another location - they will however still be in the same folder as before.
They can simply be downloaded from the one location and uploaded to the other through FileZilla - Make sure that the server is offline, and download the information in the original location, delete what is currently in the new location and upload the old files to the new location, and then start the server up.