Some ECUs reset some features. like waynnes said his and mine reset the electric window limits so have to be done manually a few times. The MAF is reset to a point along with the FBW throttle is also reset and needs to be aligned otherwise it rans badly for a few hundred miles.
mines also throws up a error code think its 30 - battery below safe voltage, or something like that.
if your worried about losing a remap or something dont be, itll not lose the map