When you hide a post in Q2A, its children are not hidden automatically*. And when running the delete script in admin, it only deletes posts that have no visible children.
However, if you need to delete a entire question you can, by hiding all its answers and comments first then running the delete script. This is a bit time consuming but currently it's the only way.
* This is actually quite logical, because if an answer has one shown comment and one hidden comment, if you hide the answer then reshow it you need to keep the one comment visible and one hidden.
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