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Active Strongholds will be unaffected by the United Forces update. If you have Strongholds from more than one Legacy coming together, both will be added to your list. If you have more specific of Stronghold (such as multiple Coruscant Apartments), they will be retained and accessible. If the combination of the two Strongholds takes you above the cap of six, they will be retained. However, you can not activate new Strongholds until you return to a number below the cap.
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