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If you upgrade from free version to the PRO, just deactivate and delete the free plugin version, then install the PRO version.
Do not worry about your settings, they would be preserved.
When new plugin version is released, do not use the standard WordPress update.
Download new PRO version from your account page and follow the same upgrade procedure as above.
If you can not see the plugin download in your account page, but you are sure that you have bought the plugin, it means that you did it in a guest mode. Do not panic! Contact the support in a chat on this site, or write an email to firstname.lastname@example.org.
See also: Free vs PRO version differences