I know that upgrading will create new default groups and policies if the originals were modified. If you are at 4.0-1, upgrading to 4.0-2 or higher will create them again. Don't know about installing the same update over it.
In the future, you may want to clone the policies and make changes the them instead (you probably realized that already). You might also want to create a backup schedule. Saved me some time before...
Tom S