Options | keepFiles - Samuel-Martineau/MC-Config-Controller GitHub Wiki

Each time you run the config-controller or config-controller.exe file to generate/regenerate the configuration for your server, all the files/folders in your servers folder (not the one in the config folder) except the server jars will be deleted. This property is to specify all the other files that need to be kept. Note that files that are in the configuration will still override the files listed in keepFiles that are in <serverNetworkFolder>/servers/<serverID>.

1. Go to the config.json file of your server/template (if you have not setup any server or any template, see Configure a Server or Configure a Template)
2. Add the keepFiles field
3. You can now list the paths of the files you want keep for that server/template only in an array format

It should look something like this:

{
  ...
  "keepFiles": ["relative/path/to/file"]
}