The following procedure will save the location, scale and rotation of your objects; but it will discard textures.
Place your level object at position 0,0,0 with no rotation and normal scale.
For each object, store the location, scale and rotation and then make mesh from the object; then use the add limb command (or append limb command if using Matrix1 utils) to add each object to the level object. Offset the limb using the offset limb command with the stored location as the parameters. Do the appropriate actions with the scale and rotation of the limb aswell. Remember to remove the meshes from memory if not needed.
Finally, use the Save Object command to save the file (There is also a Save Mesh command).
All the limbs inside the objects you appended to the level are also preserved.
