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When writing a question that has two auxiliaries, which of these is grammatically correct?

Could not he have been sick that day?

Could not have he been sick that day?

Also in formal/academic writing, would it be 'could not'? Or can I used couldn't in formal writing? The combination of 'could + not + have + been' sounds like such a mouthful to me.

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    Could not contracts before inversion if at all: He could not → He couldn't → Couldn't he but He could not → Could he not, and not *Could not he, which is generally ungrammatical, though it's possible for this form to appear in formal language, albeit quite rarely, due to Heavy NP Shift. – snailcar Sep 27 '15 at 2:46
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    And could not have he is impossible. In questions the subject inverts only with the first auxiliary, not with any subsequent complement of that auxiliary. – StoneyB Oct 7 '15 at 21:36
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"Could not" can almost always be contracted to "couldn't" even in formal writing. Usually they are only separated to emphasise the not or if you were attempting to sound archaic.

Therefore I would suggest that

Couldn't he have been sick that day?

is the best way to phrase that question.

Plus, here is some info on the Present Perfect: http://www.englishpage.com/verbpage/presentperfectcontinuous.html

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Could not he have been sick that day?

Could not have he been sick that day?

They're both incorrect. You could say any of these:

Could he not have been sick that day?

Couldn't he have been sick that day?

Is it not possible that he was sick that day?

Isn't it possible that he was sick that day?

The versions with contractions are definitely less formal. If you're trying to be formal, I would avoid them. Yes, they're a mouthful -- but then again, you're not speaking them, so they're only a penful or a keyboardful.

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