I've just replaced the passkey transponder and relearned my key. on 2002 Pontiac Grand Prix

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if I relearn another key will that effect the first key settings
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No it will not! It must have the right chip before it will work though. Another thing people make a mistake of is having the keys to another vehicle with pats in close proximity to the correct key when attempting to start their car. On the same key ring.
both keys were original, so I am assuming that they will both reset but I didn't want to screw up the first one
A relearn for the second key still seems to be my only option