I recently reinstalled IL2DCG 3.48 after a couple of years of not using it.
I generated a mission for Coral Sea. When I started the mission I could see the stock USS Lexington and the USS Generic CV (Saratoga clone).
Since my HSFX 7.0.3 has had Additional Essex Class CV's and the three Yorktown Class CV's I experimented with the ship names file and the Coral Sea mission file. First I made a copy of each original file and then I edited both files by changing the the ship associated with the name USS Yorktown to USSYorktownCV5_42 and changing the chief entry to USSYorktownCV5_42. I then generated the mission and the USSYorktownCV5_42 appears when I play the mission.
I tried to do the same for the USS Lexington by changing the ship associated with it from USSLexingtonCV2 to USSLexingtonCV2_42 (8" turrets replaced with auad 1" AA) and edited the mission file so this was reflected in the chief entry. When I generated the mission and chose to play it the USSHornetCV5_42 appears, but the USS Lexington is gone.