Of battery discharge curves

This question is to do with battery behaviour.

I have designed a simple circuit around a 16F676 that logs the discharge values of an NiMH AA/AAA cell, and then sends it serially to the PC.

I load up the battery with a resistor that is shunted across thru a MOSFET, till the battery discharges to about half the voltage, taking a reading every few minutes that this is happenning.

Now, after having mounted most everything on the PCB, I realised a two channel circuit would have been even more convenient; problem is, I would need to re-make the whole board.

So, I thought of multiplexing both the batteries; periodically, each battery would be loaded by the same shunt, operated by 2 different MOSFETs, and feeding 2 different ADCs; this way, the changes to the hardware would be minimal. A reading is taken for a battery while the shunt is across it.

This is where I need advice; as each battery would be loaded alternately for a few minutes, would I still get decent readings? I mean, the battery would not be loaded continously; when its not, it would get time to re-breathe,

Or do I necessarily have to have 2 separate load resistors, one for each battery?

Thanks for the help, in advance!

Anand