I created a couple of empty folders in a pack and then tried to delete them. They can be deleted but the next time the pak is opened they re-appear so they are never permanently deleted. I found the same to be true with a page template. When I deleted one of the ones I had dragged in, it went away but returned when the project was re-opened.
UPDATE: If you use the Remove Item from the right-click menu it will be permanently deleted, so it appears it is only if you select the item and hit the Delete button that it is not deleted. Even though it does get deleted in the list, but returns when the project is re-opened.
