I would roll back to V4 and try again. There are instructions for doing this here https://www.advancedcustomfields.com/resources/upgrade-guide-version-5/#troubleshooting
With a multisite install you could be running into an issue where there’s too much data to process. You could also be running into an issue where all of the sites are not actually getting updated, but I’m not sure about this.
If you’re still having issues contact support here https://www.advancedcustomfields.com/contact and they will try to help you with your issue.
