Hello,
All settings/ changes and website data will remain intact in the website while you upgrade to pro version of the Education Hub theme from the free theme.
However if you have made any changes directly to the theme files the changes will be lost with the upgrade.
Also, regarding the third party plugin you have used for modifications, the plugin will also remain intact with the theme switch and hence the changes made via plugins should also not be lost.
Please explain us further the changes / methods you have made in the theme files so that we could guide you further to the upgrade.
Hope this Helps,
Best Regards !!