i would uvmap the highpoly, and render out an ao map without the floaters and then render out the aos for the floaters separately, and then bake the two like the normalmap to the lowpoly
I seem to half remember that there was a trick for this besides CrazyBump which I also suggest trying. You could try, rendering it two passes. One with the floaters hidden and another with only the floaters visible (or maybe it was with shadows on the floaters disabled?). Then composite the two passes? There might be…
If you use a Max skylight and the scanline renderer, and render out a lighting map, rather than a mental ray AO map, you won't get shadow "halos" around the floaters, you'll just get shadows at intersections and in the 'bowls' of the floaters.
You can render out an object ID pass that has different colors for floaters than solid geo. Use this in photoshop as a selection mask for your AO for cleanup. This + mop's suggestion = win.
hmm, If crazy bump gives me AO maps from normals I might finally get around to buying it! I'll try merging the AO from the floaters and the base in photoshop as well though. Thanks for the help guys! I'll post results later today when I have some time to finish it.