Yen, you're colleague should take longer lunch breaks.
First, don't remove the comma. It does affectn't the tag aspect at all, but it's generally accepted to put a comma before the conjunction when you have two independent clauses. Even if you omit it, there's no resulting change to the tag.
The tag works with the final part of the sentence: THEY hadn't found it. As explained in the very solid post above, if you have a negative, you keep the same subject, and switch to postive. They hadn't, had they?
The subject is THEY, not IT, so the tag requires THEY. Your colleague's answer would work only with "but IT had never been found, had it?"
Just point out the logic of this - the tag must agree with the subject. "It" is not the subject.