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