So when you load one file from our starting setups page, its contents should completely replace the other. We've seen what you're seeing before though, although the root cause is unclear. What version of SkyView softaare are you currently running?
You can manually remove the widgets that you don't want via the engine setup menu, but that would take a few minutes in front of the display.
It might be best for you to get in touch with our tech support staff directly at 425-402-0433 or support at dynonavionics dot com.