This doesn't look like a physics problem but an algorithm problem. You might have more luck posting on stackoverflow.
Off the top of my head I'd tackle it like this:
The ball is like a ray that goes from start to finish. So all you have to do is find out which fixture is to the left and which to the right of the ray. This is a simple maths problem (looking at a sign of a determinant) considering the centers of the fixtures
in global coordinates if the line is in global coordinates too:
http://stackoverflow.com/questions/1560492/howtotellwhetherapointistotherightorleftofaline
Then everything to the left goest to Body1 and everything to the right goes to Body2.
This requires that the destroyer ball has already passed through. Won't work for "live" updates.
The general case is like this: treat the fixtures as vertices on an undirected graph. Each node is connected by an edge to its four neighbours. Now you need to find the connected components of the graph which will represent your pieces. I have no idea how
to explain it better (and the maths is too complicated for me). I usually just use QuickGraph to do the work :)
http://quickgraph.codeplex.com/
P.S: it's a calculation you would not want to do every frame unless it's absolutely critical to your game since it can be slow
