Well, if the geometry is changing, but the animation remains the same, this would be a perfect chance for a simple transition effect in post!

(ala: the Wolverene to Mystique X-men "rotating-kick" transition?)
(or the X-men2 "tent" scene... whichever makes you drool more)

1. You could simply just transition the between the 2 shots in post.

2. You could even go as complicated as multiple passes, particle "burn-away" type of transitions in Maya, lots of stuff.

List what questions bug you the most about this, and I'll try to answer them as best I can