Sometimes, a conflict between plugins and themes can cause issues with the upgrade process. You don’t need to do it on your live site. You can try it on your local site to see if the issue was caused by a conflict on your site.
Have you tried to reproduce the issue on one of the WordPress’ stock themes (like Twenty Sixteen) with other plugins deactivated? If it disappears, then you can activate the theme and plugins one by one to see which one causes the issue.
Also, could you please share the JSON or XML export file of your field group so I can check your setup?
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