Version 2 and version 3 are two seperate versions altogether as far as im aware, not that sure if there is any integration between the two.
Like the others say though providing you know your stuff it shouldnt be an issue.
If it helps though i only done V2 and only found out when i went to the brush up course and to some extent the actuall exam (im thinking Gen nav) that a couple of V3 questions were being fizzled in.
I've still got 6 to go and will probably do both when it comes to it. but even if you dont, providing you learn it, youll find youll be ok.
Good luck mate.
Dougie.