This patch allows to replace the physics Mesh on individual instances when replacing its mesh with physics option set to True.
Works with Convex Hulls and Triangle Meshes, other mesh shapes are equal all the time (like Box, Sphere and so on) and dont need to be replaced.
This new behavior is optional, though enabled by default. You can revert to old behavior by checking "Share Physics Mesh" under the BGE Physics settings for Rigidbody.
Here is also a small test file for this, just run BGE and press space multiple times.