Jeep Repair: 99 Jeep Grand Cherokee-disconnected battery knock out system?, jeep grand cherokee, car mechanic

Question
It is 3cyl., 4.0 67000 miles. Years a go someone was cleaning battery terminal on this car. Then the car did not past inspection - they ask her if someone was working on it because everything is out of cycle. Then a car mechanic ask her if somebody was doing anything. My wife 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 work on many cars and always disconnect every battery without problem. So I am confuse 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
never heard of a battery knock out system. who told u about this?
are u talking about when u have to take the jeep in and they hook it up to the computer and it will say pass or fail?  if so u cant disable that its a federal emissions function and every time u take off the battery cable or clear the codes in the computer all that info gets erased and U haft to drive it about 150 miles to make the tests run again so that U can pass the inspection.