Handy hasn't even thought to clarify that the Doctor grew the hand back. It doesn't occur to him that Cosima might assume he went about for an entire regeneration sans right hand; he was within the window of opportunity, so of course he grew a new one.

His eyes light up and he gives an undignified little prance at her deduction. "You're close!" he exclaims, delighted. "Really, that's very close -- it's along those lines. See, he aborted the process -- you can't see it now, but we'd got a good face and really good hair this last time round. Handy biological receptacle right there under the console, perfect match on the cellular level and everything, so he just...funneled the energy off. Normally stopping a regeneration will just kill you for good, but time it perfectly and bleed the energy away before the process can go beyond initial repairs to damaged cells, and you can heal without changing. The hand was only supposed to store the energy, let it leak out and dissipate on its own. But, well."

But, well, that was the painful part of the story, because it involved him only coming into existence because Donna had unwittingly put herself in harm's way. Maybe he didn't need to share that part, though. It ought to be enough that it had been an accident; Cosima had heard at least part of the mechanics behind the event. "Here I am," he finished lamely.