The Concordia-class TCS Lexington (CV-44) which appeared in Wing Commander IV is the same ship which is referenced in the novel Fleet Action. She was savaged during the Battle of Terra, crippled by internal explosions and subsequently stricken from the list. Shortly after the battle the unknown-class Heavy Carrier TCS Lexington (Armada) entered service for the special mission detailed in Wing Commander Armada's Voices of War manual. Her ultimate fate is actually unknown -- we simply know that as of 2669.098 that her status was unknown. She may have been destroyed, she may have returned home and been decomissioned after this date... all we do know is that before the end of the war the TCS Lexington (CV-44) which appeared in Wing Commander IV was rebuilt from the wreckage and recomissioned. We know that she saw action at the end of the war: the novelization claims her fighter wing was in bad shape and replaced with factory fresh spacecraft after the surrender. Captain Eisen took command when the war ended, oversaw a partial refit and then three years of patrols in and around what is now the Union of Border Worlds before the events of Wing Commander IV. Lexington's current fate is unknown (in the novel she survived Wing Commander IV, Blair having disabled her in the historical path), although there is a reference to a TCS Lexington memorial among the 'flavor text' announcements at the original wingcommanderprophecy.com website.
* - Not actually the second. The Wing Commander IV novel claims that the ship in Wing Commander IV is the eleventh ship to bear the name. The novel also notes that this tradition goes all the way back to seagoing vessels, so these eleven presumably include the five historic American warships already named Lexington (the Rec Room set in Wing Commander IV includes a framed photograph of the fifth of these ships, the World War II vintage CV-16 USS Lexington).