The transfer is lossy - whether by I2R drop in the connecting circuit or electromagnetic energy radiation or spark or other coupling. That this is so is shown a priori by the fact that you know what the end result must be (V/2 each) and that this must result in an energy decrease using any "normal" connecting method. If you use near perfect wire you get near infinite currents. Every time you have the wire resistance you get double the current and losses increase linearly with decreasing resistance (decrease with R, increase with I2).
You can get a different result using an "abnormal" method.
If you use an ideal buck converter it will take Vin x Iin at the input and convert it to the "correct" Vout x Iout at the output to allow no resistive or other losses. The result is easily determined but non intuitive. Making the buck converter non-ideal can give you a result in the 95% - 99% of theoretical range.
As we have 0.5 Joule in a 2 Farad capacitor at the end of the process we know that
U=0.5CV2
0.5=0.5×2×V2
V=0.5−−−√−0.7071V
We can try that again using just one of the capacitors. As we have 0.5 J initially we get 0.25 J in one cap at the end.
0.25=0.5×1×V2
V=0.5−−−√=0.7071V
Same result, as expected.
At first glance I thought the water tank analogy was wrong in this case, but it also works quite well for part of the problem. The difference is that, while we can model the lossy case well enough, the loss free case does not make sense physically.
ie A 10,000 litre tank 4 metres tall has energy of 0.5mgh.
h is average height = 2 metres.
Lets's have g=10 (MASCON nearby :-) ).
1 litre weighs 1 kg.
E=0.5mgh=0.5×10000×10×2=100kJ
Now siphon half the water into a second identical tank.
New depth = 2m. New average depth = 1 m. New content = 5000 litre
Per tank energy = 0.5mgh = 0.5 x 5000 x 10 x 1 = 25,000 Joule
Energy in 2 tanks = 2 x 25 000 J = 50 kJ.
Half of our energy has gone missing.
With a "water buck converter" each tank would be 70.71% full and we'd have made more water.
On this aspect the model fails.
Unfortunately :-).