Disconnecting a battery

When I buy my Spider Lusso in March I need to do some pretty major upgrades to the stereo system and was wondering, are there any adverse effects from disconnecting the battery from the car for a prolonged amount of time?

It resets the whole memory of the car- sort of puts everything back to the way that it came from the factory ;) otherwise thats about it- never had any problems when disconnecting the battery- but I'd check around- While I've never had any problems there could be some who have had them :)

The only thing I've heard is that your engine can run a bit rough for the first few miles until the ECU readjusts itself....?

I was just checking there wasn't going to be ant stupid security issues with my keys and the codes etc ;)