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Using Blender, it would be wise to work from a copy of your original blend file to use for the lightmap creation so as not to disturb the original.
Because of the nature of the lightmap effect and the way it is applied using shaders, it is required to have all the objects to be influenced by the same lightmap also mapped to the same texture.
Tip: Other blends that use a different coordinate space must be converted to the same coordinate space as the final blend that you are creating the lightmap from and also be mapped to the same texture sheet if you want to apply a single lightmap to all those object. This obviously can be a real challenge if using generic instruments.