If you're using 3DS Max, you could simply export out an env file from the source skin modifier, and then load this env file unto the skin modifier of the target mesh. The "Load Envelopes" dialog should match bones by index (skin modifier index) by default. I believe the vert IDs of the two meshes in question would need to line up for this method to work. If your vert IDs have change, try the above process with the "Load Vertices By Index" checkbox unchecked.
On the other hand if bone hierarchy is the only method you have to match bones between the two meshes and you want to automate the process of bone re-mapping, you'll likely have to come up with a custom solution using MAXScript etc.
Otherwise, I believe that both the env load dialog and the Skin Utilities tool allow you to manually re-map bones.