No, I’m not overriding $args – as per your snippet above, I return $args at the end and my code is updating 1 element of the $args array as per your snippet. From testing, using your code example, just passing the parent message ID did not hide the children replies which is why I then added in the message ID’s of the children as well.

Please can you expand on your statement about the cached message count. How do I use the hook to change it and maintain the count cache?