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Look at the thread I just posted-
It seems to be that whenever you turn off bukkit or Spigot and go to Vanilla, the Nether just resets. The DIM-1 file (the nether) just kind of goes back to default. Don't know why and I can't fix it.
The only way to fix it is to go back to the version you were on before- it will restore the work you did in the nether while keeping everything else new that you've done, oddly enough.
So I wanted to try Spigot out (I know I said Bukkit, but the same thing happens when I use Bukkit, so same difference) and I did. It worked well and then I saw that 1.10 came out. So I switched to Vanilla 1.9.4 to make sure it all worked, only to find that my entire Nether was reset to how it was in the original seed. So I switch back to Spigot/Bukkit and my work in the Nether reappears. The Backup didn't do anything (literally, it didn't even actually backup the server. Nothing changed) so I tried uploading the world files from the working Spigot server- to Aternos (while Vanilla 1.9.4 was enabled). The DIM-1 (Nether) files were slightly different in size, so I thought maybe that would work. Nope. I turned the server back on and again, the Nether had reset. It's like MC just completely ignored those files. Again, switching back to Spigot or Bukkit made the Nether reappear.
TLDR; Switching to Vanilla makes the Nether reset, Switching back to Bukkit makes it reappear
I wanna use 1.10 guys, HALP ME
It automatically sets a timer if more than one slot is empty. So the easiest way is to have 2 slots open and then enter the game and go afk. There's also an idle-kicker. --EDIT-- I think now one needs to know that 
--EDIT--
HOWEVER: Because the idle kicker and the auto shut down timer exist to keep unnecessary strain off of their systems, chances are, there's some kind of rules against this. So I would either go through the rules/agreements they set up and make sure this sort of thing is allowed first. Dunno if they even have a way of finding out, but it's nice to check anyway.
This also means that only one other person can join unless you edit the server settings, but it's just something you gotta deal with. And trust me- I've searched, there's no free server hosting that doesn't have something like this. The closest thing I found was Server.pro, which still has a timer, it's just an hour long. Unlike Server.pro, however, Aternos doesn't have any timer as long as you have less than 2 slots open. Which is nice.
