Hi @cubiix
Version 3 field types are different from the ones in the Pro version but ACF Pro contains a database upgrade tool to cater for this.
I would recommend you use the following workflow to upgrade the plugin:
1). Download a copy of ACF v4 from this link and upgrade to this copy https://wordpress.org/plugins/advanced-custom-fields/
2). After this is done you can then upgrade to Pro to ensure that your field types are compatible.
You can also read up on how to upgrade from this resource page: http://www.advancedcustomfields.com/resources/upgrading-v4-v5/ and http://www.advancedcustomfields.com/resources/migrating-from-v3-to-v4/
