Never heard of Kingdom Hearts II Final Mix+?
Sure, it was made pre-DLC and therefore existed as a separate disc release, but it came with
close to a half-hour of new scenes and made so much more sense out of KHII's story that it's kind of ridiculous. (It also added in a new story boss where originally there was only an anti-climactic cutscene-only showdown... and frustrated the heck out of everyone in the process. *shakes fist at Roxas*)
...actually, Kingdom Hearts Final Mix
also added scenes, even if they weren't anywhere near as impressive or necessary for understanding what was going on.
Likewise, Advent Children Complete was a movie rather than a game, but it also added a bunch of scenes that added context missing from the original.
In light of that, I could totally imagine Squenix adding scenes post-release. *shrugs*