I believe you can delete files even though they are not in the activity or course by using the Atto editor. You need to figure out where they are with the MoodleCloud storage page then hunt around to find the activity they are in using View in context (or just work through them all).
If the file was deleted in the editor it's still linked to the text and will not be removed when Moodle does it regular file clean up removal.
Click an existing file and open the File removal tool on the Atto editor.
In the file list at the end, you can remove unused files.