Seen this happen in dozens of games now. Whenever I take a colony with a low population nation like Sweden or Belgium, at first a few accepted culture POPs will migrate to the colonies. After a decade or two, if the POP was small like <200, all of them will have disappeared from the colony. This is with 0 wars being fought in between and no -X% population events in the colonies. It seems like my national POPs get assimilated to the native culture whenever they promote or something.