According to an 1869 reference* on Confederates buried after Sharpsburg, the Colonel and several others were originally "Buried in Capt. David Smith’s Orchard northeast corner were buried deep; the orchard has been plowed and graves plowed over, but can all be pointed out; some of the boards have been preserved at the house. Some unknown were also buried here."
[see page image here: http://www.whilbr.org/Image.aspx?photo=wccs016s.jpg&idEntry=62 ]

Then ... "In 1869 Governor Bowie requested Thomas Boullt, of Hagerstown, Maryland, one of the Trustees for Maryland in the Antietam Cemetery, employ agents to go over the battlefield and mound up the trenches and graves of the Confederate dead, to make careful notes of the locations and, as far as possible, identify the dead. To accomplish this task, Moses Poffinberger and Aaron Good of Sharpsburg, both well acquainted with the battlefields, were engaged. They visited the trenches and graves of Confederate soldiers in both Washington and Frederick counties, Maryland. This list, published as ordered by Governor Bowie on May 1st, 1869, is the result of that labor and it is believed includes, with a few exceptions, all the Confederate dead buried on the battlefields of Antietam, South Mountain, and Monocacy".

"Those Confederate soldiers who were known to be buried in Washington County [which encompasses Sharpsburg] were finally buried in the Washington Confederate Cemetery in Rose Hill Cemetery, Hagerstown. The dedication took place June 15 1877 ..."

*The book: "A descriptive list of the burial places of the remains of Confederate soldiers, who fell in the battles of Antietam, South Mountain, Monocacy, and other points in Washington and Frederick counties, in the state of Maryland"; from the Western Maryland Room of the Washington County Free Library, Hagerstown.

All of the above has been posted online on WHILBR - Western Maryland's Historical Library, here: http://www.whilbr.org/confederateSoldiers/index.aspx

Hope this helps.