I have an encrypted rclone.conf symlinked from another dir using GNU Stow. If I edit rclone.conf using “rclone config” a new file is created, the symlink is broken, and the original rclone.conf in the outside dir remains unedited.
Hmm, if you are using an oauth based remote (eg google drive) when rclone needs to update the token in the config file it will save it again. Does that work correctly?
You might be better off symlinking the directory that the config file is in rather than the config file itself.