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To change your flagship, go to shipyard -> fleet and look on the right. You will find three slots, two of which will be occupied with your ships. Choose the second ship (Archangels II) and select 'remove'. Go back to the fleet menu, tap your old ship (Archangels I) and then swap with the other ship. Voila, new flagship.

(Source: forums.toucharcade.com/showthread.php?t=110587&page=9)

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Q: How do you flagship a ship in galaxy fantasy iPod?
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