When you select to edit a Free Design layout you will be asked to make a duplicate of the original show and provide a new name to the edited layout. ALL content, settings and information associated with the original show will be copied to the new show and so all your work will be preserved.
Note: when you edit a free design layout you will NOT be able to delete any of the existing panels in the layout - only add new panels to the design. This ensures that there is no orphaned content left in the system from a panel that you delete from the original show. We would advise that if you want to delete any panels that you start with a new design instead.