If you update to the most current version of WordPress and Yoast SEO, does this resolve the issue?
1. Check for conflicts.
2. Check for JavaScript errors with your console.
If you find any JavaScript errors related to Yoast SEO or if there is a conflict with a plugin or a theme, you can create a new GitHub issue for our developers. Please report the issue to a third party developer as well.`
can you share the code that update the meta keywords and desc, there are couple of ways, i cant explain why but some works better then the other.