Hello, George- The loss of the USS Atlanta off Hatteras (former CSS Atlanta) did not occur in 1865. I do not know if she had been registered as a merchantman. I recall running across a ship by the name Atlanta, of northern registry, though this one, of the tonnage mentioned in your reference, was used as a troop ship to Wilmington, N.C., 1865. She is not the same ship.
The USS Atlanta was renamed the "Triumph", under Haitian registry, and sank off Hatteras in December of 1869.

I'd like to know how Lieutenant William C. Whittle, Jr. managed to disappear from the C.S.S. Atlanta before capture by the monitors Weehawken and Nahant in Wassaw Sound. He had been captured and paroled by the Federals after the naval battle on the Mississippi in April of 1862. Another capture would have doomed him to imprisonment without hope of parole. Believe me, I've dug to no effect. Perhaps he represented himself as someone else. Close as the monitors were during the engagement I cannot believe he managed to go over the side and escape. Any pieces to the puzzle out there?