Is it possible to bake two different lightmaps for one scene and than switch them on the fly?
Yes, it is. To load lightmaps on the fly you should load them to lightmaps array.
Of course you should bake and save them before (to resources or to asset bundle, for instance).
Keep in mind, that each lightmap is an atlas. So, to apply two different sets of lightmaps properly you should bake them with lock atlas option. Instead that, you can save index and offset of each object and load them later, but i think it is not optimal solution.