He felt an odd, unfamiliar tugging in his chest that he imagined was probably sympathy. Perhaps remorse. But he hadn't meant to cause this. A part of him wanted to allow John to believe the charade. Maybe it would make him feel better, in the end. To think he had his Sherlock back, at least for the moment.
But he couldn't. He'd promised he'd come clean when he'd decided to help heal the little girl, and he'd done so. Now everyone knew, including Captain Pathetic, and he couldn't go back on that. Besides, the man had suffered enough. It would be unfair to make him think he was going mad all over again.
"I'm afraid Sherlock isn't here," he said slowly, in his cool and collected voice. Which, unfortunately for John, still wasn't all that different from Sherlock's. In fairness, he'd been able to keep up the charade for so long because he and the detective shared quite a few qualities other than just their faces.
He stepped a bit further into the room, allowing the man in the bed to see him in a clearer light. The differences were there for those who knew either of them well. Which only left John. He knew Sherlock well, and was likely the only one who did. And him... Well. No one knew Khan well. No one in the last three hundred years for him.