If you Bulk Edit custom post types, it deletes any terms that were saved for each post.

To reproduce:

1. Select multiple posts in the post list screen
2. In the Bulk Actions select box choose Edit
3. Change something like the author or status
4. Click Submit

It will remove whatever terms those posts had assigned.

This can be fixed by adding this:

// If posts are being bulk edited, we don't want to do anything.
if ( ! empty( $_GET['bulk_edit'] ) ) {
	return $post_id;
}

In the first line of the save_single_term function in the class-wordpress-radio-taxonomy.php file.