Just an update, the author of backupwordpress is about to release an update which he says will fix the problem of the wp-admin .htaccess file being deleted when backups are triggered. He was able to replicate the problem himself. Please see this thread here https://wordpress.org/support/topic/backupwordpress-is-deleting-wp-admin-htaccess-file?replies=9#post-6489964 for more information.
Thanks.