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I'm not very sure, but I think the "he/she had" structure is more colloquial/informal? Or maybe I should never use that construction when asking questions?

Here's an example sentence:

Her hypothesis opened a door to new questions: was her problem some sort of genetic disability? Or she had/had she inherited this behavior from her parents?

  • English usually uses subject/verb inversion to form questions, so it's Had she [done this]? (not She had done this, which is a statement rather than a question). It's not normally "colloquial, idiomatic" to use the "subject+verb" sequence in the context of a question. Native speakers do this sometimes (using rising intonation to signify that it's supposed to be a question), but often it's just seen as an indicator of "non-native speaker", so you should try to avoid it. – FumbleFingers Dec 20 '18 at 16:08
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"Or had she inherited it from her parents?" is grammatically correct. "She had ... [done something] ?" is not acceptable in a normal question, even informally.

  • Not relevant to the grammar, but as far as meaning goes, it sounds like your might want to eliminate the "Or" in your example, since it makes your statement sound like "genetic disability" and "inherited from parents" are two contrasting possibilities. In fact, genetic disability is often inherited from parents. [Just a note on the use of "or", not meant to answer your query about word order in a question.] – Lorel C. Dec 20 '18 at 16:24

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