This is our site : https://bioprotectionportal.com/. We have changed indexing manually for homepage so it changed for all pages but from last 10 days site was showing no index no follow and we thought it has stopped indexing when plugin updated. So can you please check if there is something wrong with plugin or what so that next time this problem will not come.
Kindly know that updating Yoast SEO doesn’t cause noindex. To make sure your site is not set to noindex, kindly head to WordPress dashboard > Settings > Reading > Search engine visibility and check if the checkbox “Discourage search engines from indexing this site” is unchecked.
I was unable to replicate this from my test site, so it can be specific to your setup. If this happens again, you can check settings like the wp-config.php, plugins, database for something uses?update_blog_public?and sets the entire site to private.