Suppose the following sentence:
"Aren't the headers not covered by copyright?"
Is this sentence correct?
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Yes, it's correct. But if you get at yes or no answer, I bet you won't know how to interpret it.
If you do away with the contraction, your sentence is:
Are not the headers not covered by copyright?
This means what you are trying to confirm is that the headers are not covered.
This is confusing, but it isn't a mistake unless you're trying to confirm the opposite. If you don't mean to have a double negative, you have the choice of including the negative before or after 'the headers', so instead use either
Aren't the headers covered by copyright?
Are the headers not covered by copyright?
In either case, you aren't opening up the respondent to a yes or no answer. If you want a clear answer to your question, you're better off saying:
Are the headers covered by copyright?
If you want to get across the fact that you were under the impression that headers are not covered by copyright, then you should say:
I was under the impression that the headers are not covered by copyright. Are they?