It sounds like you are using a selection filter to control what is exported to Navisworks. I can think of at least two ways to save your selection in the view.
1. After using the selection filter to adjust what elements are selected in the view, click the Temporary Hide/Isolate command (the eyeglasses in the View Control Bar), select Isolate Element, and then click the Temporary Hide/Isolate command again and click Apply Hide/Isolate to View.
Note: If you want to maintain an unchanged version of the view, you can duplicate the view before going through the steps above.
2. In the 2013 software after selecting the elements, click Save (on the Modify Ribbon tab, Selection Ribbon Panel), type a name for the selection, and click OK. When you want to restore the selection (with nothing currently selected), go to the Manage Ribbon Tab, click Load (on the Selection Ribbon Panel), select the saved selection and click OK.
Note: The second option won't work as well right now if you don't have the Navisworks exporter for the 2013 software.