When you upgrade from free to pro you basically just need to make sure that you transfer over all the customizer settings from the free version to the pro. There’s a handy plugin that can export all the settings and then import it to pro.
The process would be as follows:
1. have the free theme active
2. install the export/import plugin and go to Customizer / Export,import settings
3. export the settings
4. activate the pro version of the theme
5. import the settings you exported in step 2 in the customizer
If you are still missing anything you had setup with the free version let me know and we can take a look.
Please make sure you have a backup of your existing theme files and database in case anything goes wrong.