Battries, as MrChips figured out, and i confirmed, above.I still don't know if you are charging batteries or capacitors.
i welcome corrections.(mis)use of the term "ground"
it's a good idea. Who's idea is it?the idea of suppressing or correcting the use of "ground" where it is unnecessary or confusing is not my own.)
Are you distinguishing a physical earth ground vs. power-supply "common"? Is "common" the preferred term in this case?a true, physically verifiable ground
Look at your original diagram.To use just 1 switch/cell, i'd have to keep the ground-lead of each cell connected to ground of the charger permanently. Instead of moving the ground from cell to cell as i charge, I would only switch out the hot lead.

The sim i'm using cannot model battery chargers. I'm substituting caps for the sake of discussion. I understand with batteries there will be resistance that is not included in my rough model using caps.You started with two capacitors in series, now they are batteries?
Correct.You make it sound like you have a variable supply and it will change dependent upon the charge needed so not to damage the battery. And you want to charge one battery at a time.
Why not charge them both at the same time, but not in series? ...You hook the power supply with the positive to the most positive connection of the series batteries.Confused-- you just said "not in series".
You mean i can charge a battery with a negative OR a positive supply? Neat!Instead of isolated grounds, you have a common ground with a positive and negative supply.
Yep, i realize that cannot work. That's why i started this thread.If you "keep the ground-lead of each cell connected to ground of the charger permanently" (i.e., the red node) then you short out the bottom capacitor.
Yep, the Maxim circuit i posted in the OP is a charge pump, according to Maxim. It currently looks like my best option.You can use circuits, such as flying capacitor circuits and other charge pump circuits