Doubt this is your man; Missouri SOS archives site lists a Henry E(H on card image)Skaggs, enlisting Co A, 1st Reg Cav Volunteers (Union!) Capt Sterlin on Sept 15 1862 at Spingfield MO Mustered out Little Rock Ark. June 14, 1865.
Greene County is a long ways from Otterville, Cooper Co. There were a number of Skaggs families in Jefferson Co MO in 1860 which is close to St Gen county. In the 1860 Census there is 16 year old Henry Skaggs, son of Henry and Mary Skaggs (owners of 2 slaves on 1850 slave schedule) in Plattin Twshp, Jefferson Co, MO.
If he was an irregular fighting against the Union in or around Ste. Gen county I would lean more towards him being from Jefferson County than the North central part of the state. Some unit or other name/date info would be helpful.