Some dates to put your search into perspective.
The Battle of Bentonville was fought on March 19th, 20th, and 21st twenty or so miles south of the town of Smithfield which was on the North Carolina State Railroad running between Raleigh and Goldsboro. On March 21st, General Johnston withdrew his forces from Bentonville back north to Smithfield, and the western wing of General Sherman's army continued northeastward to Goldsboro which had been their objective before being ambushed by Johnston. General Johnston's army remained camped at Smithfield through April 9, 1865 when they completed a substantial re-organization and consolidation of the remnants of the old Army of Tennessee. General Sherman’s army was reunited at Goldsboro during this same period.
On April 10th, Johnston's army began an orderly withdrawal from Smithfield along the railroad through Raleigh towards Greensboro. Sherman's army followed and General Sherman first learned of the surrender of General Lee on April 11th when he arrived at Smithfield. Pontoon bridges were laid across the Neuse River and the Federal army occupied Raleigh on April 13th. The Confederates completed their withdrawal to Greensboro by April 14th.
The fighting that took place on April 12th was rear guard skirmishing between the two armies as they shifted to the west. The Military Atlas of the Civil War (General Topographical Map Sheet III, Plate CXXXVIII) shows Swift Creek entering the Neuse River just below Smithfield and running in a more or less straight line northwestward towards Raleigh. It ran parallel to and south of the North Carolina State Railroad which was the Confederate line of withdrawal. Swift Creek protected the Confederate left (southern) flank all the way to Raleigh.
I read Lieutenant Wiley C. Howard’s account of the skirmishing (April 12th along Swift Creek). There is a 1st Lieutenant W. H. (T.) JEFFRIES listed with Company E, Power’s Regiment, Mississippi Cavalry on the NPS Index to the CMSR. But there was no Crute’s Unit History to see if this unit was in anyway part of the Jeff Davis Legion cavalry. He was the only Mississippi cavalry officer surnamed JEFFRIES that I found in the NPS database.
Robert Crook contributed the following passage from the memoirs of Volney D. Fowler, a Mississippi cavalryman present during these final days: >>>"Our army continued its retreat before the vastly superior numbers of Sherman, the cavalry hotly skirmishing every mile of march. We crossed Cape Fear at Fayetteville. Then across Neuse River where we burnt the bridge...At Bentonville, near Goldsboro, on the Neuse...(we)were in battle three days. Here gallant Lt. Charles Metcalf was killed...but, at the surrender, there were present only a dozen men. As Lt. Metcalf had just been killed, we were without a commissioned officer." <<<
This narrative condenses nearly two months of operations into a few lines. The Confederate army safely reached the vicinity of Greensboro, North Carolina by April 14th and no major fighting took place between the two armies after Bentonville on March 21st. General Johnston and General Sherman negotiated a surrender agreement (there is a long story behind this) which was finally signed and dated April 26, 1865 at Greensboro. The Confederate soldiers present for duty in North Carolina, including those in hospitals, and those away from their unit on details, were paroled over the next several days. On May 3rd, the remnants of the Army of Tennessee marched to Salisbury to draw rations, and on May 5th they departed Salisbury for home.
Taking the Fowler narrative at face value, one could conclude that Lieutenant Charles Metcalfe was either killed in action at Bentonville on March 19th, 20th, or 21st (and buried somewhere on the battlefield), or that he was mortally wounded and died in a Raleigh hospital to which the Confederate wounded were taken. If taken to Raleigh his burial in Oakwood Cemetery should have been noted. However, you have a copy of Colonel W. F. Waring’s diary asserting that Lieutenant Charles Metcalfe was killed in action along Swift Creek on April 12th. One of these narratives is wrong.
Lieutenant Howard could have made a mistake in identifying the Lieutenant from the Jeff Davis Legion as “Lieutenant Jeffries”. Can you account for 1st Lieutenant W. H. (T.) Jeffries, Co. E, Power’s Regiment, Mississippi Cavalry and show that he was not in North Carolina either with a Mississippi cavalry company, or serving as a staff officer? If Lieutenant Jeffries was the only cavalry officer from Mississippi with that surname, and you can account for him elsewhere on or about April 12th, 1865, then you can eliminate him from contention as being the Lieutenant "Jeffries" that Howard remembered. It would strengthen your contention that Metcalfe was killed at Swift Creek on April 12th and hastily interred in the same grave with Lieutenant Tom Dunnahoo.
Hope this helps in some way to sort things out! Keep us posted on what you learn!