Take the pack that lasts a few hours, and clone its EEPROM onto the other two. Then change the cells. itll be fine afterwords. 

Also before you do this, make sure the good battery is charged all the way up. Then disassemble. That way the eeprom is left in a state of "full charge" 

Then clone eeproms, swap the cells. Let  the rebuilt batteries die and recharge. it will recalibrate itself.