The closest I've been able to find to a resolution has been the Gatherer rulings on [[Gisela, the Broken Blade]]:
In a Commander game, your commander may be Bruna, the Fading Light or Gisela, the Broken Blade, and the other may be in your deck. If they meld into Brisela, Voice of Nightmares, Brisela will also be your commander; but if Brisela leaves the battlefield, only the card chosen as your commander at the start of the game may be put into the command zone.
That just says that the melded card is a commander, though, and not what happens when the melded commander does combat damage. From the Comprehensive Rules, it seems to come down to what's meant by "the same commander":
903.10a A player who’s been dealt 21 or more combat damage by the same commander over the course of the game loses the game. (This is a state-based action. See rule 704.)
A few other CRs would seem to shed light, but I'm still not quite sure of the resolution:
903.3b If a player’s commander is a meld card and it’s melded with the other member of its meld pair, the resulting melded permanent is that player’s commander.
903.3c If a player’s commander is a component of a merged permanent, the resulting merged permanent is that player’s commander.
903.9c If a commander is a melded permanent or a merged permanent and its owner chooses to put it into the command zone using the replacement effect described in rule 903.9b, that permanent and each component representing it that isn’t a commander are put into the appropriate zone, and the card that represents it and is a commander is put into the command zone.
That was my initial thought, yeah, but I couldn't find any explicit ruling to that effect; only that both halves of the melded card should be able to go to the command zone in the weird partner/meld case (as per 903.9c applying to each half separately).