Well, when you switch to Pro version you do not need to fully customize or rebuild your site. The data that you have added will be there.
In other words, your theme option customizer values would remain the same just that your sidebar widgets will be reset to default. Therefore, you need to re-organize the widgets after activating Pro version if widgets exist in your current free version. So widgets are the limitation in this case.
Note: Widget resetting on theme switch is the default behavior of WordPress and not a specific limitation of this theme.
Hope you will proceed accordingly by taking note of widgets prior to upgrading to Pro version so that you can easily recreate them later.
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