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You are right that a drift alignment will destroy the star model. But a subsequent star alignment cannot change the polar alignment if you don't touch the alt/az bolts. The star model might want to tell you that you have a PA error (Maz and Mel) but you can ignore that if you trust your drift alignment.
Its just as (or more) likely that the reported PA error after a star alignment is due to inaccurate centring of the stars in the eyepiece during the star alignment (including not clearing any backlash).
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