Dennis,
By 1863, most company flags had been sent back home and retired. A few remained in regimental baggage. After April 1862 the issuing of company flags pretty much ceases as regimental battle flags of the various patterns start showing up and the whole point of that was to attempt to standardize battle flags within the respective CS armies.
Perhaps some company flags were taken at Vicksburg but the bulk would have been regimental building and garrison colors.
greg Biggs