I bought a second battery for my EVO so I could swap out halfway through the day, or whenever I needed to. Now I understand that changing your kernel can give you bad battery life for a few charges as the kernel "gets used" to your battery. One of my batteries is the stock 1500mah while the other is 1750mah. Would switching out the batteries cause my kernel to "get confused" by the changes and lower my battery life? I've "trained" the batteries correctly by fully depleting them when I first got them and everything and am still getting great battery life on CM7, this is just more of a curiosity
The kernel actually uses the current voltage of the battery to determine its charge level. Therefor, no matter what capacity battery you put in the phone it should accurately display your remaining charge as long as the battery is broken in, which is what you did by doing atleast one full deplete/charge cycle.