As the free version and the Pro version are two separate versions of the plugin then you need to deactivate the free version prior to activating the Pro version. You can keep your settings by following these steps:
1) Deactivate the free version
2) Install and activate the Pro version
3) Delete/Remove the free version
Alternatively, you can check the Preserve settings when plugin is removed setting which is at the bottom of the Misc tab on the plugin’s Customize page.
Either of these methods will carry your settings over from the free version to the Pro version.