You could do this:
- load the new OBJ
- save it as an LFS object
- load your original LFS object with the cutouts and mappings
- delete all triangles and points
- create new subobject at 0,0,0
- load - as a subobject - your OBJ that you resaved as an LFS object
- merge subobject into main object
At this point you have all the points and triangles from your new obj, and you still have your cutouts and mappings.
- load the new OBJ
- save it as an LFS object
- load your original LFS object with the cutouts and mappings
- delete all triangles and points
- create new subobject at 0,0,0
- load - as a subobject - your OBJ that you resaved as an LFS object
- merge subobject into main object
At this point you have all the points and triangles from your new obj, and you still have your cutouts and mappings.