Which flag would depend on which ship. Lynch had found five French tri-colors in a locker at Gosport. He designed a flag for the fleet with a Latin cross of 11 stars on the blue field of the flag. The Sea Bird's flag is at the Museum of the Confederacy. The Beaufort also flew one of that design at the battle of Hampton Roads. The Raleigh may have flown one as well. The Curlew, Ellis, and Fanny flew flags with three bars (two red, one white) with a blue canton with various numbers of stars in varying patterns. The Curlew flag is in private hands. The Ellis flag is displayed in a dining hall at Annapolis, Maryland, in a case that also contains her Union flag. An oil painting of the Fanny in the NY Historical Society collection shows the Fanny's flag. I can't speak for the Forrest, Black Warrior, or Appomattox.