The National Archives has the records of the Provost Marshal's Office in Record Group 110. Section 110.3.2 contains the records of the Deserters Branch. These records are described at:
http://www.archives.gov/research/guide-fed-records/groups/110.html#110.3.2
Alice J. Gayley
Pennsylvania in the Civil War
http://www.pa-roots.com/~pacw/