in that if the original thread has been posted by a moderated user
That doesn't sound quite right.
It must have started out visible in the beginning otherwise nobody else would have been able to see it at all in the first place surely? This thread would have just consisted of his complaint and any responses from the staff? The thread was started during the time he was being moderated IIRC.
You did however appear to remove the moderation during the time of the conversation. Since something that was visible ended up hidden I can only assume that disabling the moderation for the user has actually ended up with the thread being incorrectly hidden, which to me sounds like a bug.
In any case why have anything that affects an entire thread? If a user is being moderated and their individual message passes moderation then does the overall thread even matter or deserve any attention?
Incidentally whilst we're on the subject of bugs the ads at the top of the page are still broken. This time it's for an HP 'Accelerating Health' (WTF does that even mean?) advert. Pretty much every single large advert has had this issue, so it doesn't look like it's anything to do with any one specific advert & any custom behaviour, rather it seems related to its size.