Not sure what you mean by "car system", but no. Things like the odometer, ECU and everything will be fine. This will reset all memory functions in the car back to their factory settings... I.E. the trip computer will reset (including gas mileage, etc.), the radio will reset to factory settings, etc. I would imagine the nav. unit would completely reset as well, so you may lose any saved locations you have in there (not sure though, as I have never had a car with a factory nav. until this one and have not reset it).
It's not detrimental to disconnect your battery, as most car maintenance is strongly recommended to be done without the battery hooked up (to prevent a short) even in non-electrical maintenance.
