The batteries are in series, so its hard to know see how a flash could damage one and not the other. The batteries have been tested continuously at 2 amps, I think that's far more than a flash would draw.
If you have a meter, it would be something easy to measure. I had 3 of the Energizer Advanced Lithium's on my desk, along with a old Triplett meter I just bought. Open circuit voltage was 2 volts on two of them and 1.6 volts on the other. All had been used a equal amount, so there appears to be substantial variation. I think the 4th battery was tossed and dead. Sometimes things lay around here too long.
Interestingly enough I saw this too before I started using Eneloop. Often when I tried rechargeables the batteries were empty really fast. Yet when I put them in my charger only one would show being depleted while the other ones usually looked on the okay side. (I only did this a couple of times however since there really was no point of using the rechargeables with so little capacity)
Never had that issue with my Eneloops however, they all seem to discharge at the same rate.