Can’t configure mods on dedicated server

Running into an issue where the linux server refuses to take most config files for no apparent reason and keeps things at default. I've tested locally and the configs update and store properly in ModConfigs. When added to the server they just refuse to load most of the config files as if they dont exisit. I've added the files everywhere I can think of (root, ModConfigs, Mods, Saves) on the server with no luck and I'm losing my mind here.
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