How do I apply the changes to a mod after I configure it through the files?

I put some mods into my server and I decided to change the config of some of them after starting my server, So I stopped it, pulled up the config, and changed some things. After I did I went ahead and saved the changes and started my server back up again, but when I went into it, none of the changes were there. It was as if I never edited the mod's configs at all. Do yall' know how have the changes apply when i change and save the config files for the mods?

When i checked the files after the server was online again, and all the changes for the config were still there.