Hi, I am inclined to believe my ancestor did indeed serve in two units. There is a reference to Pike County MS in each of his files and this is where he was from. His family showing up with him in one unit lets me know this is the right ancestor. It is his wife who filed for a pension who states he served in another unit. Also, there is a old family story that one of the brothers fought for the north. This may be where that story comes from.
I looked at earlier research on this ancestor and another Civil War researcher gave me some information on how or why the two units show up in his file.