If you have the hk setup like mine you have protection circuits, so if there is a short, ie blown speaker or loses wire or metal touching the positive lead it will kick into protection mode and disable some speakers, happened to me when i installed after market speakers. They worked fine and a few weeks later the leads at the back of the speakers were apparently touching the door metal, vibration made them wear through the paint a little and caused a short and before i knew it, only had half my speakers working. Check connections and wires for shorts, check for really blown speakers, cause if they are just a little blown doubt it would cause a serious enough short to kick in to protection mode. If no shorts then looks like its your amp. Maybe deck, but i don't know too much on these bmw decks so i wouldn't quote me on that.
2001 325 Ci