i think it depends on who you take it to, and how good the installer is.
i know when i had my 2001 jetta, first thing every asked me was if i had the stock amp in the trunk. nobody wanted to touch my stereo if i had that amp.
it can be done though, a friend of mine has a 2003 330 with the HK system, he put in a different amp adn a sub for that matter.
i think if you just want to swap the amp, it just has to be compatible with the new one.
you should check out some quality audio store to find out for sure.
i like the one i went to with my jetta, it was on steeles in between young and bathhurst.
i can find the name and adress if you want.