Not sure if it is just me but i have a temporal recruit and a gamma recruit that suddenly stop having an active shuttle. not sure if it a bug after the latest update. but i notice i don't see my shuttle listed in status unless i switch over to it and use it as a main which was the old way of doing thing like 5-6 years ago.... it has been awhile. only list the main ship you are controlling/flying physically.
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https://www.arcgames.com/en/forums/startrekonline/#/discussion/1263452/shuttle-not-shown-in-active-status