I can try to help out on what I know.
1) I did not see the 80th NY aka 20th Militia on that list. They captured a "1st National Stars and Bars", Blue Canton, 3 stripes, red-white-red, 34 by 70, with 11 Stars. I believe that was either BG. Kemper's Brigade flag or BG. Garnett's Brigade flag. BG. Armistead brigade was to far to the left and I ruled that out. I am leaning more on BG. Kemper.
Source: http://www.civilwarnews.com/archive/articles/picketts_flag_return.htm
2) "27th Pennsylvania, July 1st, Brickyard". The 27th PA was on the far left in Colonel Coster's brigade and they could not shoot straight but on at a right angle. Their was a gap between the 154th NY and 134th NY and only 50 men from the 27th PA heard the order to fill in that gap. The 6th NC and 21st NC were stopped cold, while the 57th NC went around the 134th's NY right flank and rear. I highly doubt the 57th NC lost that flag. A Union soldier wrote "They had so many flags every so rods". I believe the 6th NC (95%) and 21st NC (5%) chance of losing that flag. The flag certainly was not the main battle flag, for on the night at on Culp's Hill both regiments had their main battle flag. So the flag in question must be a guidon, or something else.
3) 8th Ohio captured the 28th North Carolina's flag. That flag was then handed to one of BG. Hay's aides who then handed it to BG. Hays. He looked at the flag and saw "Harper's Ferry" on it and then he dragged the flag "To erase the stain". In the Hollywood movie "Gettysburg" they show BG. Webb (Late Brian Pohanka) and his aides dragging the flags, that is untrue.
4) #20, "19th Massachusetts". Now the 19th Mass did not captured that flag. Major Rice, pointed his pistol at a Union enlisted soldier and demanded the flag. The soldier and his regiment is unknown. Major Rice was wounded, went back to his home in Massachusetts and took that flag with him.
5) 53rd VA, Listed as captured by the 71st PA. Major Rice wrote in the 19th Mass's regimental history, "BG. Webb handed me that flag and all credit is due to the 72nd PA." Also the 19th Mass's regimental history claimed they captured, 14th Va, 19th Va, 53rd Va and 57th Va. (53rd Va of course was handed by BG. Webb).
6) #50, Captured by 126th NY, I noticed a Confederate Regiment in BG. Davis' brigade not listed as losing a flag. The 2nd Mississippi, certainly they did have a flag in the charge. I have read the 2nd MS had at least 78 men in the charge, only one single enlisted soldier made it back without a scratch. I am just suggesting that 126th NY may have captured the 2nd MS flag. I highly suspect that they did lose their flag they had in the charge. (Gregg, the 2nd MS flag captured at the R&R Cut, was that a new flag or their old flag?) Which ever it was, the back up flag would have been the opposite.
I am curious about the divisional flags, (Pickett's, Heth/Pettigrew and Pender/Trimble.) I noticed none of those were on the list, I am no expert at all on Confederate division flags, if they were in the charge or not. If we look at all of those brigade flags, Kemper, Armistead, Garnett, Archer/Fry, Pettigrew/Marshall, Davis, Scales/Lowrance and Lane, certainly several were captured.
It is a combination of where Union regiments were on the line and reported capturing a flag (That are still unidentified), process of elimination and "Other" types of flags other then the traditional Battle Flag, Brigade Flag etc. Some of those Confederate flags I typed in this post are purely just suggestions, finding the proof is always the hardest part.
Have a good day,
Shawn Prouty