When the rotalists move inside their ships to another location its because they are sure that they gat already taken the last location
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U also can beat them by fighting inside the countryside, if u got a colony deep in land, u can chose to set the front line between the ports and this city... but u will have to counter attack and u will lose many colonies. And it isnīt better than attack when they move to land, u will got high loses even wining the war, its another deseperate measure to high challengers.