Think of MineOS as, say, a single program in a location /usr/games/minecraft, like how Microsoft Office exists.
If Word stops working, you don’t need to scrap the entire build. MineOS is just one program that runs alongside hundreds of others that make up your Linux Distro. As is always the case, scrapping a build is never what I recommend, because a) it is overkill and b) discourages seeking out the actual problem and finding the solution.
That said, do whatever you feel helps get your server back up and running properly most quickly, even if that is scrapping it.