The Raleigh County Court records might mention the family. If both parents died or were killed, it is possible that guardians were appointed for the children. If Samuel owned land, it could have been sold by representatives on behalf of the children.
Bear in mind that most WV Counties did not keep birth and death records for some period during the Civil War. Not finding death records does not mean that something extraordinary occurred. In most places our WV ancestors lived in this period, there were frequent epidemics of typhoid, cholera, and other diseases caused by lack of sewage treatment/sanitation.
Either way, there is no substitute for going directly to the treasure-house records. If you don't find something in Raleigh County records, it would be logical to look in Floyd County for the same sorts of records (except possibly land deeds); it is possible that Samuel and Sarah moved.