I am having a similar problem with the Aquarius escort and Chevron separation. The sections will detach and fly off. but then disappear. they do not reappear until I call them back to attach.
Just tested Hestia with MVAM console in ISA STF, tried 2 separation methods, both times the ship animation displays, but then both sections take off straight and fade out never to reappear again or help in battle.
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Another topic where many others report the same problem http://www.arcgames.com/en/forums/startrekonline/#/discussion/1225783/t6-andromeda-saucer-separation-possible-bug