You do need to save the OBJ (using a different name to the original file), you then need to edit a copy of the CR2 to refer to the new OBJ file.

UVMapper can save UVS files that can be passed on to others so that they can apply the new mapping to their own copy of the OBJ (see the ReadMe for this item for an example of the process -> http://market.renderosity.com/mod/bcs/index.php?ViewProduct=59018).