Yes I did find it. My server config was just the default so I simply deleted everything that wasn't the server. The odd thing is when I moved this world off the official servers to my system (because it was laggy) I had to change what world was selected in the server config. Later is when I made a creative world to test things and for some reason a day later when I had the server restarted it replaced it. I can only assume maybe I had made a server with the singleplayer world through in game which replaced at least the server config?
Regardless I can for sure say I am scared to make any more worlds lol. Everything seems fine with the server and hopefully I can find out how to avoid this in the future. I probably would of quit for a while because we had made so much progress.