how is it working?
it's not

(at the moment)
-edit
(sure psp and 3ds are different things, but the same general idea applies) i'm sure something similar could be done one day if it gets to it, with the psp, some games needed updates to go online, and, i forget the reason, but, playing the .iso, you could not download the update, or, you could not use the update, something like that. most times all an update is, is a new executable file, to replace the old one. eventually, we were able to replace the old executable in the .iso with the new one from the update patch.
if we are able to decrypt roms (people can, not publicly), decrypt .cia files too, i assume the same people who can decrypt roms can decrypt these, then, i imagine that just the same thing as the psp scene did, we can do here, and rebuild the rom with the new update, this way we would be able to have things like out of region updates installed, i've seen lots of people upset that they can't play monster hunter online ha.
we can't do this yet, but i reckon it's very feasible.
or, as soon as we can install .cia files, then it's all taken care of
