When you are satisfied that new server is running as it should, that all content has been migrated, switched users over to the new server, and are no longer using the old server, you can remove files from <new_appdata> that are no longer needed.
q <appdata>/DefaultParameters.xml - These are now in the JSON file.
q <appdata>/CEP/Applications/ - Applications are now stored in the repository.
q <appdata>/CEP/Archive/ - If you migrated the change history, this is also in the repository now. Otherwise you can keep it if you want to go back to an earlier application version.
q <appdata>/CEP/Datasources/ - Data sources are now also in the repository.