The Jenolen is holding the Dyson's sphere's gate open with its shields and is unable to move because the engines have failed. LaForge tells Picard that he has to destroy the ship in order to get through. So Picard orders the transporter room to beam Scotty and LaForge out of the ship. Then he orders Worf to fire the torpedoes. You can see, that the shields are still online. How can they've been transported through the shields? There is no indication that the shields of the Jenolen ever been dropped.