I discharged a ship from my fleet because I needed to make some room. Not realizing that my Disco Dual Beam Bank, Disco Torpedo, Borg Regen Shield, Borg Deflector, Lukari Impulse, and Lukari Warp Drive were still on this ship. They did not transfer when I activated a different ship.
Are these items lost? I thought the game pulled off any equipment still on the ship, and pit it into you inventory when you dismissed a ship.
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The game only moves equipment from ships that are put into drydock. Any ship you delete, usually have it's equipment deleted alongside with it, I think it depends on what kind of ship you delete and where you delete it from. Usually the warning that pops up says whats going to happen, so clicking OK without reading is never a good idea.
Also it's a good idea in general with STO to always move things around manually, never expect the game to do it for you. Especially when you delete things, probably the items are lost forever.
Try to make a support ticket and ask, in the meantime do NOT get a new ship with the same name.