Ok well I'm sorry but your configuration sounds like its in "a mess" - and since you started this discussion by talking about manually editing configuration files I wouldn't be surprised if something like that is the root cause of your problems/confusion.
If I were in this position I would be stopping all services, destroying all services, redeploying all services, running health-checks and so on until my server was in a stable, clean state - but if you are not familiar with doing things like this then I would absolutely NOT recommend you do this on your own.