For some reason, he disappeared from his company on February 22, two days before relocating their camp, and four days later, his mustering officer recorded him as having deserted. There must have some reason for recording him so, usually, his absence as such, would first be termed "absent without leave," and sometime later changed to "deserted."

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The following "Record of Events" is given on the muster roll of December 31, 1864:

My Company has bin no general engagement since the last Muster The company was in the Reconnoiceance made near the New Markets Hights about 9th Dec before that time and since it has bin on the line between the Charles city and Williamsburgh Roads was sent to Gordonsvill to Repel a Yankee rade on 22 Dec Return to camp on 28th Dec an mustered to day by Lt Col Wylie

S E Carrol, Lt, comd, Co, H

The following "Record of Events" is given on the muster roll of February 28, 1865.

This company has been in no engagement since last muster Remains in camp on Williamsburge road till 24 Feb 1865 when we moved to the right and took position on the line near Fort Gilmore two men have Deserted since last muster Feb 28 1865.
http://www.researchonline.net/sccw/rosters/5thinfh2.htm

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He very well could have returned to his unit prior to Appomattox, as he so states. Unfortunately, the next bi-monthly muster would have been conducted the end of April. The Army of Northern Virginia had by then been surrendered and paroled. Hence, we would not have had a record of his presence.

On April 9, 1865, his regiment surrendered 19 officers and 263 men.

By virtue of the fact that he was granted a pension, I would feel his record has been corrected.

You should be able to find out more information as to his service at the end of the war through the testimonials by his comrades in his pension file. These records are available through the service noted in the Red enclose box shown above.

Note also, three other Lipsey's also served with Newt.

Lipsey, Ira, enlisted in Company E, 5th SC Infantry April 15, 1861, was discharged at Richmond, Va. December 23, 1861 "by reason of disability,"

Lipsey, John, Company H, 5th SC Infantry was transferred to Co. B, 18th South Carolina Vols. about November 15, 1864

Lipsey, James, born in Union Distl., SC, enlisted April 13, 1861 in Company H, 5th SC Infantry at Union Court House, died of Typhoid Fever at Moore Hospital, Manassas Junction February 27/28, 1862, father Richitson filed for his pay & allowances due

Note also:

Baldwin, James J., III. The Struck Eagle: A Biography of Brigadier General Micah Jenkins, and a History of the Fifth South Carolina Volunteers and the Palmetto Sharpshooters. Shippensburg, PA Burd Street, 1996. 471 p.