Auto Parts: 99 Jeep Grand Cherokee-disconected battery knock out system?, jeep grand cherokee, car mechanic

Question
Compstall. It is 6cyl., 4.0 67000 miles. Years a go someone was cleaning battery terminal on this car. Then the car did not past inspection - they ask my wife if someone was working on it because everything is out of cycle. Then a car mechanic ask her if somebody was doing anything. She mention battery again and mechanic say: "that it! Now you need recalibration because battery should never be disconnected". She say it cost her $150 because they connect computer and reset everything to previous setting. But her owner manual dose not mention any other suggestion except that you need to clean battery terminal. I think meany times mechanics like to blame people unnecessary to secure their job. Somewhere around that time my wife went also for alarm recalibration and she thinks all that because of that battery. They recablirated alarm except passenger side door, they won't open until we press button again. My friend, certified auto mechanic, now working as a buss mechanic for 20 years, say he don't get it, work on many cars and always disconnect every battery without problem. So I am confused now. Thinking maybe that someone made some kind of short or by accident put wrong terminal on wrong post. Or maybe maybe the battery was disconnected for to long? My friend want to make tune up on this car and want to disconnect battery but I told him no, because I need to find your opinion first.  

Answer
Mario,

Any time you disconnect the battery on a newer, computer-controlled vehicle for a length of time, the PCM will revert back to its original engine, fuel, and emissions settings.  It does indeed take a few miles/days of driving the vehicle again to get the PCM to "re-learn" both its environment and your driving style.

Also, many vehicles with factory alarm and anti-theft systems have codes programmed into the stereo.  Any time you disconnect the battery, the code will need to be punched back into the radio.  Every vehicle I've ever worked on - that code CAN be disabled.  Mine are all disabled on all my vehicles for this reason.  What you can do is either find out how to reset the vehicle's code yourself or have the system disabled.  Your choice.