When you duplicate a layout, it refers to the same table via the same table occurrence as the original. Thus, all relationships etc that work with the original layout should also work with the duplicate of that layout. What won't work will be any scripts/buttons that navigate to the original layout. If you were to delete the original and keep the copy, such would need a quick update to connect to the correct layout.
But each time you select a different theme for a layout, your database file get's a bit larger. I suggest that you open a copy of your layout, select different themes (without editing the layout objects) until you find one you like.
Then select that theme in your original copy of the file and discard the copy where you experimented. You can select the theme for the current layout or a copy created by using Duplicate layout.
For More Information see: Repeated Theme Changes Bloats File Size
This is one of many acknowledged bugs that can be found in the Known Bug List thread here in the Report an Issue section of the forum.
It can also be downloaded as a database file from: https://www.dropbox.com/s/jt09b82i0xijbu3/FMP%20Bugs.zip