How do you determine that a cell is going bad?
I would run both of them on a cycle program, at the same rate of discharge to the same voltage cut off.
But if they are the same brand and capacity, I would guess that the one reaching the LVC is the worse of the the two.
I assume that you are balance charging each time and also putting the batteries at the proper storage voltage between flights? Both are important
Heat, and deep discharge are the two biggest killers of rechargeable batteries, I think. 

If your charger can do it, and most can, you could charge both packs, then discharge each right after on the same rate, to the same cut off voltage. That would probably confirm your suspicions of which pack is in worse shape(probably the one that cuts out in flight)