Farcry was made by Crytek and published by Ubisoft.
Crytek then started to make CryEngine2 and a new game called Crysis, which will be published by EA.
The Farcry name is owned by Ubisoft, presumably as part of the publishing deal with Crytek, where they published the game and had the rights to the name.
Ubisoft, as a result, is making Farcry 2 using their own in house engine, since they have nothing to do with Crytek anymore (since Crysis is being published by EA).
There is a Farcry 2 website which includes developer blogs, one of which is about the engine Ubisoft are building specifically for Farcry2. (Brand new engine for the game)
It is almost exactly the same as other games such as Operation Flashpoint, made by Bohemia Interactive and published by Codemasters.
BI then made a new engine for their new game, which got called Armed Assault, published by other publishers.
Codemasters owned the rights to the Operation Flashpoint name, and are making Operation Flashpoint 2 completely independently of BI and using their own engine.