For any Googlers still arriving in this thread, the above fix is no longer applicable.
I disabled ACF 4 before doing the database upgrade for v5 Pro and found my field groups had disappeared.
The ‘Upgrade Database’ prompt checks an option named ‘acf_version’ in wp_options, so I reverted that to my 4.x version, enabled both the 4.x and 5.x plugins as per the upgrade documentation, and the Upgrade Database prompt reappeared and ran successfully.
