The Phoenix was not part of Farrand's fleet surrendered at Nanna Hubba (Nana Hubbard?) Bluff. My mistake.

Warships and Naval Battles of the Civil War, Tony Gibbons: indicates Black Diamond, a sternwheel warship built in 1865, was surrendered in May 65.

Naval Official Records: indicates Black Diamond was sidewheeler (2)

Iron Afloat: Lists 5 ships surrendered, including 4 warships (Black Diamond, Nashville, Morgan, Baltic) and transport Southern Republic.

Naval Official records: describes each of the 4 warships surrendered, including Nashville. There were several transports surrendered in addition to Southern Republic, including the 4 blockade-runners Mary, Virgin, Heroine, Red Gauntlet, that had performed picket duty. Farrand represented these were army (rather than navy) ships. Heroine was surrendered at Mobile and did not move up the Tombigbee.

However, there was no threat to Mobile in 1/65, so it doesn't make sense the Phoenix was sunk then. Here are some clues that make me think it was earlier.

Warships and Naval Battles of the Civil War, Tony Gibbons: indicates Phoenix was destroyed August 1864, a better date considering the threat at the time. Also,

Mobile Bay and the Mobile Campaign, Hearn: on Metacomet's reconnaissance to Mobile on 8/15/64, Farragut "discovered a large vessel which he erroneously identified as the unfinished ironclad Nashville filled with stone and brick and sunk across the main channel". Since Phoenix and Nashville were both large sidewheelers, this was probably the Phoenix.

Regarding the Nashville, I've seen some evidence that she was built at Montgomery. The Nashville was also certainly surrendered, not destroyed. There is a possibility that the site is confused with another ship. Nashville was launched while flying the Confederate flag at the Montgomery waterfront on May 7, 1863, before the cheers of hundreds, and quickly sailed downriver to Mobile.

Iron Afloat: "on August 19 (1862), he (Farrand) contracted for one large sidewheel ironclad and two 150-foot propeller ironclads to be built at Oven Bluff on the Tombigbee river. Early in September he negotiated for another sidewheel vessel to be built at Montgomery". Some confusion may have been due to the fact there was another (after the Tennessee) large ram under construction at Selma.

Iron Afloat: A week after the fire (of caissons at Mobile) he (Buchanan) received word that a large sidewheel ironclad similar to the Nashville, under construction at Selma, was damaged beyond repair on her launching".

Warships and Naval Battles of the Civil War, Tony Gibbons: indicates Nashville was surrendered and later (1867) sold.

The Battles Opposite Mobile (Confederate Veteran), William Lochiel Cameron: you may have seen this outstanding account of an officer aboard the Nashville during the end of the war. He indicates Farrand took the warships to Demopolis, then sailed back to Nanna Hubba to surrender. Cameron writes that "on the evening of the 10th of May, 1865, everything having been arranged, our vessels were formally surrendered".