The Minecraft vanilla server software provided by Mojang stores secondary worlds differently than Spigot and some other third party server software. If you're switching from the vanilla server software to Spigot or Paper, and you want to keep using the existing nether and end worlds you will need to do the following. Note that the Paper server software handles this automatically, so if you're using Paper, nothing needs to be done. 

  1. Stop your Minecraft server
  2. Connect to FTP using an FTP client of your choice
  3. Look for the folder for your world, the default name is "world" unless you've manually changed it. Go inside the directory, in the default case, /world
  4. The world directory for a vanilla server will have two folder inside of it, one called DIM-1 (so /world/DIM-1) and DIM1 (/world/DIM1). The nether world is DIM-1, the end world is DIM1
  5. Move those /world/DIM-1 and /world/DIM1 directories to the main server directory by dragging and dropping them in your FTP client to the ... at the top of the directory listing, this will put them in the directory higher up
  6. Once they are in the main server directory, example /DIM-1 and /DIM1 instead of /world/DIM-1 rename the DIM-1 folder to world_nether and rename DIM1 to world_the_end, this way your main server directory should have /world, /world_nether and /world_the_end directories now

Switch your server jar to Spigot, Paper, or your own jar file and start the server. It will be using those worlds now properly.

If you want to switch from Spigot or Paper to Fabric, you would need to do the following.

  1. Stop your server
  2. Delete the existing /world/DIM1 and /world/DIM-1 folders
  3. Copy or move the /world_nether/DIM-1 folder to /world/DIM-1 (this is the nether world)
  4. Copy or move the /world_the_end/DIM1 folder to /world/DIM1 (this is the end world)
  5. Start the server
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