Paul, you are right, backups in this case should go only to external Hard Disk, as per explanations Davo gave to me here:
http://moodle.org/mod/forum/discuss.php?d=200616#p886451
And ther you should be able to delete them, without affecting the Moodle Database, which, in this case, seems not to be tracking all those files.
Let us know your experience, after testing the different options.
Rosario