FlyThemesHi
This is happened because the clovemix free versions and pro version are very different not because of look but for functionality since pro version has many functionality that is the reason it created separate tables in the database so you may need to add your content again when you activate the pro version but you free version settings will not be erased it will shows whenever you activate free version. The options settings of any theme will be visible only for that particular theme only the WordPress contents like post, pages and menu are the same for all so you need to add your settings and content again for the pro version this is required only once for this theme so whenever you will get the update theme of clovemix pro in the future you will not to be add the content again it will saved automatically.
For any help and support mail us at: support@flythemes.net
Thank You