Ben,
You shouldn't have to change it. Especially if it's outside your scope of work (which it sounds like it is) you're not required to make it conform. However, if you were making some other change to that fan box, and not upgrading the motor, then you'd be in trouble.
Simple rule for C&I is: If you're touching it, you need to make it meet LEED requirements. If you're not, you don't.
Paul