You shouldn’t ever use root to run Minecraft servers or anything related for security reasons, and MineOS is designed to run servers as a user, not as root and doing so you are bound to run into plenty of problems regarding permissions, which can actually cause the problem that you ran into (which is not being able to save).
It depends, if you intend to use plugins then go for it, if you intend to keep it all vanilla then leave it vanilla. Spigot does have it’s performance tweaks and all but I guess it just depends on how you want your server to be. If you do opt for Spigot though, you might want to check out Paper which is just like Spigot, but with more performance optimizations. You might also checkout the post below, which is basically made for starters and people with low-end systems, and it works atop existing servers.
But in your case I’d suggest you to create an archive of the server’s files then create a new server from that archive, and it should solve your save-all problem, I’m not sure you could recover lost work though.
If you decide to try out the server project, all you have to do is drop the zip into /var/games/minecraft/import then from the UI, import a server, and then copy the existing world folder over to the new server.
Or you could just extract the contents atop the existing server but you’ll have to set the max player count, server name, etc minor things, but I suggest you don’t extract atop the existing server because you’ve been using root to host the server and it wouldn’t solve anything doing that.