It seems there’s something that prevents ACF from updating your database correctly. Could you please update the database on one of the WordPress’ stock themes (like Twenty Sixteen) with other plugins deactivated. If the notice disappears, then you can activate your theme and plugins again.
If the issue persists, could you please check the error log on your server?
If there’s no error log, could you please open a new ticket and provide temporary admin credentials to your site? You can open a new ticket here: https://support.advancedcustomfields.com/new-ticket. Also, please don’t forget to explain the issue again and provide the link to this thread.
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