After February 1864 rolls for this regiment were either lost or destroyed, so it's not possible to know exactly what became of many of the men who belonged to the 46th Georgia. Since Joseph McCall doesn't appear on Federal prisoner-of-war records or in final parole registers, it's possible that he became a casualty during the Atlanta campaign, or the Tennessee and Carolina campaigns which followed. Perhaps a casualty report printed in a Columbus newspaper lists his name.
According to the 1860 census schedule for Georgia, two men named Joseph McCall lived in the state: one in Talbot County; the other in Appling. Was yours the Irish overseer who lived in Talbot County? That's not far from Webster County, where Joseph McCall enrolled in 1862.