I haven't tried it, but you could try creating the default (say THT) PCB within the project, open PCBNEW.exe (from the KiCAD install), create a new PCB based on the netlist from the project, save the (presume SMT) PCB into the project folder, then you should, in theory, have both PCB's within the project.
I don't think KiCAD has back / forward annotation so I don't think you will sever any links between them, it all used to be done by manually importing the netlist.
Try it!