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I don't know much about superconductivity, but shouldn't you be able
charge the capacitor in the absence of resistance (superconducting
circuit). Then, since the energy loss doesn't depend on R, you would
still have to get 1/2 CV^2 for the energy stored on the capacitor. But
where does the other 1/2 CV^2 energy go, in this case? Or maybe the
energy stored on the capacitor in the first place is actually CV^2, not
1/2 CV^2, even in the presence of nonzero R.