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While she didn't touch him, most people "feel" when someone is super close to them. I know I do... then again this is Shinichi

Yes, according to the mock scenario that was shown in the manga file and in the anime, she never ONCE made contact with Shinichi. Why would he feel anything if she was over him? He likely could hear her clothes, but there would be no reason for him to assume that it was her clothes, instead of his own or Ran's. So in a pitch black tunnel, with all senses skewed except for touch (pitch black kills sight, smell obscured by wind, hearing obscured by wind, taste... well that's kinda useless here, isn't it?), Shinichi, who never felt her as she was over him, could not know it was her without the proper evidence.