I have posted here that three of the regiments of Pickett's Division did not use the June, 1863 issued flags at Gettysburg. These are show in the late Richard Rollins book "The Damned Red Flags of the Rebellion." This would indeed explain why examples of these flags were captured later in the war.
Included in Pickett's Division at the time of the flag issues were the brigades of Gen. Corse and Gen. Jenkins. Their troops received these new flags as well base on the existence of the flag of the Palmetto Sharp Shooters of SC in private hands today. Both of these brigades were left behind in Richmond and Pickett's Division went into PA with only three brigades. Most ANV divisions at this time were four brigades.