I just tested this (using Database>Move/Copy) and the first to find flags were preserved in the destination database. Is it possible that these waypoints already existed in the destination database and you had either "Only Flag" or "Ignore" checked under "If the waypoint already exists...." on the Move/Copy database dialog? If you tell GSAK to ignore existing caches in the destination database, no information will be transferred from the source for that waypoint.
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