No, this is precisely what happens.Given good quality real world components I could charge up one capacitor to 100volts, connect through a series of wires of different lengths and diameters, some wound as formal inductors, some straight to a second similar capacitor and then disconnect.
In each and every case I would walk away with two capacitors charged to pretty close to 50 volts.
Are you suggesting that somehow the energy is not 5000C before the second capacitor is connected and 2500C after ?
With real world components then the missing energy has almost all been dissipated in losses in the conductors and dielectrics. It's possible that with long wires you may have launched some into the aether.
Something similar to this happens billions of times a second in your computer, the dominant loss is CMOS devices is in driving load capacitances. It doesn't matter how small they make the resistance of the FETs, the power lost in taking the load capacitor from 0V to 3V (or whatever) and back again is constant.