discharging and recharging degrades the battery. if they are discharged at different rates, then they have a different amount of degradation. the larger the difference in degradation, the worse off you are. as a battery degrades, its mah rating will decrease. that leads to the two batteries reaching low voltage at different rates. then the less degraded battery will pick up the slack there will be added strain to the battery
devils advocate - wont they reach equilibrium at some point?
lets say 100% is a brand new battery, and 0% is at which point you recycle the battery - talking about overall battery life here, not life on a single charge.
you start with one battery at 100 and another battery that you've put a few cycles through sitting at 98%.
Assuming you are pulling somewhere around 20amps, one battery can handle that.
The dominant battery will do more work causing it to degrade faster, lets say the stronger battery now at 98% and and the weaker is at 97%.
Run that scenario one more time and they are both at 96%, at which point they have the same "degradation."
Like I said, I'm playing devils advocate here, I personally would buy brand new batteries and run them as "Til Death Do Us Part," but still seems like a plausible scenario.