If you multiclass into a class archtype and the archtype replaces an ability for one you previously have, can you keep the base ability instead? For instance, my Level 1 Magus decided the Magus life was not for him and at level 2 I switched to alchemist with the grenadier archtype. The Grenadier archetype replaces the brew potion feat with a proficiency in a specific martial weapon. My one level in Magus means I am already proficient in all martial weapons, so do I take the brew potion feat, or do I just get nothing? Or is it a GM call?
you get nothing
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You get exactly what you said, proficiency with a specific martial weapon. Just because you already had proficiency with all martial weapons, doesn't mean you don't get another line that says "Martial Weapon Proficiency (specific weapon of choice)"
But in effect, Zautos is right, you net nothing additional.
just like how a fighter with martial weapons and full armor and shield doesn't get anything when they go paladin. If you get something you already have then it effectively does nothing.
Conversely, if you take a rogue archetype that replaces Sneak Attack but not Debilitating Injury, you could have a useless ability unless you regain the lost ability in some other way.
Trapfinding without Disable Device as a class skill is less effective but not totally useless.