If you clean correctly it will only help. The premise behind barrel break-in seems to be that most factory barrels have tiny imperfections. Shooting rounds through the barrel polishes these imperfections out through heat and pressure. If you do not clean between rounds then copper that gets deposited into these imperfections will stay there and those imperfections may not get polished out.
I've only broken in one barrel before but it seems to be working. Ive noticed that as I've been cleaning, the barrel has been getting progressively less fouled for a given number of shots and the deposits seems to come off more easily than before.