Problem with Jetpack Stats

I recently changed the theme on my blog. For this, I created a separate WordPress installation using cPanel since I didn’t want to take down my site while I worked on a new theme. Then, once the new theme was customized I copied all the folders into the old installation on File Manager. Now the problem is, ever since I did this, Jetpack is only showing results for the new theme. Does this mean I’ve lost all my previous analytics? Is there anyway to fix this? Really need some help.