I guess I will chip in here, these guys are too nice.
You bricked you server by taking root. I’ve done it too. Don’t worry, lesson learned. Move on.
Here is how to move on: When you ‘save the archive’, use the MineOS WebUI as intended and as JayMontana36 knows the permissions for that archive will be correctly saved in the ‘archive’ folder and when imported into a new server, the permissions on the new server will be correct. You will have lost some work, but OK. Move along. (You may have to manually move the newly made ‘saved archive’ to the new servers ‘archive’ folder so that it can then be ‘imported’, depending on how you proceed. The point is do all of that as “mc” or whatever username you have chosen, NOT as root!)
So, make a new server and import your archive and everything will be as it should.
Until you decide to take ‘root’ again. Of course you can, and to do one or two tasks you might even want to, fine. Restrict your actions to that and that alone because as stated by the men above: MineOS is by design supposed to be used by a user, not root or you may risk bricking your server.
Thanks and Good Luck!