1997, ES300 - disconnect battery

:screwy: I removed the battery from my car and when i put it back, the electric system in my car became weaken ... some of the lights came up and I had to take it to the dearler to check. It cost me $318 for them to tune up my electrical system. Someone said, if you disconnect the batter from the car, when u put it back it will mess up your electric system . .. is that right ? To me it not make sense because if your car has problem with the engine and you take it to dealer to fix, they also disconnect the battery before doing anything. after the fix the engine problem ur car will have electrical problem ? It's weird ...
My car has 65k miles on it. Is anyone has the same problem by disconnect the battery from the car ? .. thank you for your reply.. !

With BMW's, you have to wait three minutes between ignition turn off and battery DC or it can cause trouble with the various microprocessors that are found on all cars now.