Possible spoilers for GI Joe: Retaliation follow.
It was a terribly kept secret (not helped by the marketing) that Duke died early in GI Joe: Retaliation. Channing Tatum, an embarrassing connection to the first film, would show his face and be ritually slaughtered to let everybody know that this wasn't the same Joe as last time. I'm sure Channing was okay with that.
But then a funny thing happened - the movie got yanked a mere five weeks before release. There are a lot of reasons why, most of which boil down to the film probably being bad and Paramount getting cold feet, but there might be an unexpected side effect. While the studio pretends they're converting the film to 3D the reality is that they're doing massive reshoots - which may include saving Duke's life.
Could Duke still be gravely injured at the beginning and be comatose for the film? Might he actually show up more in the movie now that Tatum is gaining some level of fame? Either option seems reasonable. And I'm sure Paramount is weighing them both, as reported by The Hollywood Reporter.
I wonder if we'll ever see the original version of GI Joe: Retaliation. Now it'll become a lost film. In twenty years young film nerds will be trying to track down ancient .avi files of it.