I may have had a similar issue with the launch of our new website. Our outside developer told me he turned the Allow setting on after go-live. A week ago he installed Yoast. Today, I found our Discourage Search Engines setting was on.
Our developer says that installing Yoast has a default ON setting to Discourage Search Engines. That does not sound right. Thoughts? Is this right?
Also want to follow this issue to see how your situation is resolved in case it happens to our site. Thanks.