The Zone of the Enders HD Collection ran into a bit of drama when it was discovered there were some negative technical disparities between the original games on PS2 and their Xbox 360 and PS3 updates. Siliconera did the translation work of a recent podcast, where Kojima stated the team is reworking the game and will release a patch for the PlayStation 3 version. There's no mention of an Xbox 360 patch. No release window for the patch was mentioned.
Kojima also mentioned that "Enders Project," a sequel in the franchise, has had the entire team taken off of it. He is currently re-evaluating what to do with the series.