This is a Minecraft (mojang) thing, and not something to do with MineOS. A quick google reveals a couple of post (but nothing offcial ) that states that the secondary world files for “End” and “Nether” gets reset. I have, however, not heard anything from the users of “my” servers that they have been reset. That, combined with a lack of official forum posts from the minecraft forums leads me to think that something else is happening.
Are you switching server types? (F.ex from Bukkit to Vanilla?) The different servertypes may store their alternate worlds in different folders. If that is so, it should be enough to rename the old “nether” and “end” folders to the new name so that it matches what the server is looking for. You can see this by listing files and folders, and looking for a double set of Nether and End folders with slightly different naming conventions.