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Yeah - thats what I would have assumed it did - I would have been very surprised if I ran into that behavior. IMO, as long as the serial has already been set up, and setup is called again, only options specified in the second call should be applied.
Maybe you'd need serial.setup() (no arguments) to return the serial to it's default state (just like pinMode with no mode)
DrAzzy
@Gordon
IIRC it changes them to the defaults (lowest numbered/ported pins capable of doing what was required). Now you mention it, I could change that behaviour so if no second argument is supplied it uses the one that was supplied last time (which is saved anyway, so the Serial port can be re-initialised when code is saved).