now that I've deleted the Jetpack plugin - I've lost all the customized CSS I entered in the "Edit CSS".
If you reactivate Jetpack and the Custom CSS module, your customizations will be back.
Where are these files stored? within the Jetpack plugin folder?
Your custom CSS changes are stored in the wp_options table of your database. Each custom CSS revision is stored as a post using the custom CSS post type. As a result, your changes won't disappear if the jetpack plugin is deleted from the plugins folder.