The WordPress Toolkit will force upgrade all plugins despite what the Auto-update is set to. setting.setting in WP itself. On a customer site, this causes rewrite_rules in the wp_options-table relating to custom post types to disappear. This is quite likely related to a must-use plugin that the customer has created for single-sign-on.
This can cause issues with the rewrite rules in the wp_options table relating to custom post types disappearing. This issue is currently being reviewed by the WordPress Toolkit team and we recommend following this article for updates regarding this.
None at this time.