I read a lot, there was a Technical Service Bulletin from Jeep, that warned against connecting and disconnection the PCM plug under power (with the key in run or the battery connected). It can mess with the programming. Something about causing pulses to the power circuit or something. Just something I read in passing, wasn't really paying attention, as I was looking for something else. Was just thinking, moisture in the connector could possibly do the same thing, cause a pulse or surge.
After disconnecting the battery, there is a procedure to follow. Reconnecting it and letting the motor just idle is supposed to be bad for it. I really don't remember the recommendations. I usually take it for a drive with little to moderate stop and go and then a moderate run up a high speed road at 35-60-40 until it is at operating temp. Works for me, I'm guessing the relearn procedure was recommended to avoid running it at idle or a constan RPM, to give the PDC a variety of driving inputs to recalibrate or something. Just a WAG (wild arses guess).
The alternator in the wifes 96 was acting up, overcharging and it seemed different voltages, most anytime I looked. I was wondering if it was the gage, the alternator or the regulator. I disconnected the battery for awhile, checked my Alternator connector and PDC connections, inspected the wiring and reconnected the battery. The problem disappeared. I really don't know if I fixed it or it fixed itself. But a couple of months later the battery failed, that may have been part of it.
I really haven't had that much trouble out of our 96, I've had a lot more experience with the old Renix's.