I understand your question, when S2 is closed you get a voltage of 3.3V f we consider charge conservation and another one if we consider energy conservation. But connecting a capacitor in parallel with an ideal power supply is forbidden, at time zero when S1 is closed the voltage on the capacitor should be zero, so you are doing a shortcut to an ideal voltage power supply, maybe that is the origin of the incongruences. you cannot shortcut an ideal voltage PS as you cannot leave open an Ideal current PS (i.e. you cannot put a coil in series with an ideal current PS)
Also you cannot put in parallel two ideal capacitors, the redistribution of charge implies an infinite current when S2 is closed.
On a real situation with resistors involved there would not be conservation of energy since some of the power would be dissipated in the resistors, the final voltage of the capacitors would be approx. 3.3V