Cal here from Shopify, thanks for reaching out to us. That's a great question, however, each copy of a theme is a fresh, blank slate. I'm afraid you will need to apply the existing changes to your new, fresh theme. The good news is that you don't have to immediately publish the new theme, and you can work on it in the background until it's ready to roll! Then when you're all set to switch over, you simply click 'Publish', and that new theme becomes live.
It's a common occurrence that a store might be working with a few different themes at once, designed for different times of the year and different seasonal demands.
Best of luck with your new theme!