The ship was designed for hit-and-run attacks, and thus was lightly-armored, lightly-shielded, and had little laser weaponry. This put the vessel at a disadvantage in a straight-up fight and Dee was concerned that even a Longbeam cruiser and a Jedi Vector would be capable of taking out her flagship.
After the ship was destroyed during the Battle of Galov, the Jedi Order salvaged the ship's Path drive, which they installed into the Ataraxia so that the Jedi could travel to the Nihil's Great Hall in No-Space and bring Dee to justice, as Jedi Master Avar Kriss believed Dee to be the key to the Nihil's weapon they used against the Jedi.