The destruction of the Missile Boat facilities was a series of sneak attacks committed by forces led by Rogue Grand Admiral Zaarin, on the Empire's Missile Boat production facilities that forced a recall on all active Missile Boats.
Details of the attacks are unclear, but what was clear was that the causualties inflicted by Zaarin's forces was estimated to be in the thousands.
Because of the facilities destuction, and combat losses on various missions, as well as the unrelated theft of the Missile Boat prototype Sealion by the Rebels as well as its recovery, Emperor Palpatine ordered all avaliable Missile Boats to be recalled until the Rebel Alliance was eliminated at the Battle of Endor. However, because Palpatine was killed in that fateful battle, the recall was never lifted and the Missile Boat would, likely, never see actual combat again.