Bad batteries will not kill your transmission. If your system voltage falls too low, the TCM will set a Low Battery Voltage fault, and may put you in limp-in, but that will not kill the trans.
Which two gears did you lose? How does the trans drive now? What does it do (or not do)? No shifts into 5th or 6th? Got any faults or CEL? Does it shift normally 1-2-3-4?
Which two gears did you lose? How does the trans drive now? What does it do (or not do)? No shifts into 5th or 6th? Got any faults or CEL? Does it shift normally 1-2-3-4?