The question being: “Why/How did Regina choking the shadow actually hurt it? Its a friggin magic flying shadow afterall.
I think you’ve sorta answered your own question though. It’s a magical flying shadow. It clearly already doesn’t operate by the rules of normal shadows. Why can it be choked: well the same reason it can fly, carry small children and full grown men, speak and have intelligent thought. *magic*
While I like your explanation, I think the honest answer here is magical shadow is magic.
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"He was a lot of things to me" "The only conclusion was love"