It looks like my server was killing the update query that was taking too long.
[Tue Nov 29 21:00:14.452382 2016] [:error] [pid 14427] [client 64.21.199.186:21049] KILLED QUERY (204070 characters long generated in /nas/wp-content/live/swimswam/wp-content/plugins/advanced-custom-fields-pro/admin/install-updates.php:428): SELECT term_id, meta_key, meta_value FROM wp_termmeta WHERE term_id IN …
