I just started to use FileRise and found, that the config.php file should be retained on release updates.
This is what the example scripts do.
BUT: The file became very large over the last releases and contains global helper functions, that need to be added on version upgrades.
It would be better to have a pure "configuration" file, separated from global helpers.
I would suggest to either separate the functions into "globalhelper.php" and to import them in config.php or to have custom settings (like Uploads folder, limits and so on) in a separate custom_config.php and to import this in config.php.
BTW: Could you please re-open #110 - I do not have permissions to do so.