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Question about The Starfarers of Catan Flight Phase - Is it allowed to build in the Catanian colonies at a later moment if there is more than one free colony intersection?

Answer

No. No matter how many colony intersections remain free in the Catanian colonies after the starting setup, you are not allowed to found additional colonies in the Catanian colonies afterwards - not even if the requirement that in a 3-player game in each planetary system one colony intersection must remain free were met, and this requirement need not be met during the starting setup.