Just be vewy, vewy careful not to swap out a spell that's a requirement for the PrC!
Complete Warrior reinstated the rule that if you lose access to a PrC requirement, you lose access to all class features except BAB, Save bonuses, hit dice, and skill points.
So if you're an Archmage, with "knowledge of 5th-level or higher spells from at least five schools", and you trade out Wall of Force (your only 5th-plus Evocation) for Cloudkill (joining all your other Conjurations), you lose everything Archmage provides. Including all the "+1 spellcaster level" bumps.
-Hyp.