With 3 x LiPo in series and no load connected, charging them one at a time is entirely acceptable.
- Note that LiPo and std LiIon are essentially the same for the purposes of this question. Key differences may be the maximum allowable charge rate as a proportion of full capacity. Std LiIon is usually charged at C (1 hour rate, ma = mAh capacity numerically) initially. Some few may allow 2C and some want as low as C/2 but usuallyy C. LiPo vary to some extent with manufacturer's boldness and higher rates may be allowed. See data sheet in all cases !!!
The charger need to be truly floating with respect to the battery when disconnected so that any one cell can be accessed at a time without interaction.
You would want to avoid having to use the combination while batteries were in a different state of charge - although even this would do no harm as long an no cell was discharged fully. The danger in discharging a series LiIon battery combination with different states of charge is that exhaustion of any one cell is not readily detected without monitoring each cell individually. If you DO monitor each cell for minimum voltage on discharge and stop discharge when this occurs, then even discharging a differentially charged battery is acceptable.
As you are going to need to connect to the cells one at a time, you could consider making up a switchable connection to the charger, and then rotate between charging cells reqularly. The excessively enthused [tm] could could easily automate this with eg relays (or electronic switches if more venturesome.)
Swapping between cells every few minutes say should still produce an acceptable charging pattern due to the well behaved nature of Lithium chemistry cells when charging (as opposed to eg NimH where this would be a bad idea. For the first 70%-80% of charging from fully discharged the call is in constant current more and then changes to constant voltage, decreasing current when maximum voltage is reached. Both these stages would be well handled even if you swapped batteries every few minute.
Parallel charging with a single cell charger is not possible without isolating the cells electrically. If the charger is not capable of providing more than Imax for any one cell then there would be little advantage in doing so compared to the occasional rotation method mentioned above.
If the charger was capable of providing say 3 x Imax then parallel charging would be faster than one at a time BUT current balancing would be absolutely essential.