The 5th Conn and 28th NY are known to have lost flags at Cedar Mountain. Some sources say that 3 flags were captured and some say 4 flags were captured. There is at least one other that is unknown.
The 7th Ohio infantry lost the most men at Cedar Mountain. Of 300ish they lost 182 (some say 200) either way only 100ish made it out. Flags?? That's how it always is, did they lose a flag??
The 5th Virginia infantry regiment certainly captured all of the flags. Robert K. Krick Sr. book "Stonewall Jackson At Cedar Mountain, is a huge help. On page 212, Krick, wrote "Stonewall brigade captured all of the Federal flags taken on the field."
Now some officer in Branch's brigade took one of the flags from a member in the Stonewall brigade. That flag is unknown (to me).
Page 219, confirms that the 7th Ohio helped save the 5th Conn's Regimental flag, after the color-bearer was wounded.
Page 220, confirms that the 28th NY lost their Regimental flag. "Someone pulled the regiment's flag off its staff."
Page 245 is very interesting. In 1883, Colonel Edwin F. Brown of the New York regiment addressed a gathering of the Fifth Virginia veterans with recollections of the twenty-one-old events. "You captured our brave boys by the hundred," Brown said, "and with them {our} flag." "When the Twenty-eighth's color sergeant went down with wounds through both legs, he tore the flag from its staff and tried to hide it under his coat. The flag's bulk thwarted the wounded sergeant; a Confederate saw the edges sticking out and took it."
On May 22nd, 1883, veterans of the 5th Va returned the flag to the vets of the 28th NY.
"The Stonewall brigade captured a third flag, in addition to those of the 5th Conn and 28th NY, although its identity was not established."
Major Williams asserted that his regiment (5th Va) captured all three flags. Colonel Ronald credited the 5th Va with two of the three flags. He also wrote that the third flag was "improperly" confiscated from a private by an officer after its capture.
Stonewall Jackson's official report confirmed the three flag's identities (including one nonidentity) and simply cited the Stonewall brigade as their captor.
Private Narcissus Finch Quarles captured all three flags. He was in company "E", 5th Va. He also captured 19 Union pows and had the three flags on his shoulder. He took the flags to Jackson's Headquarters.
Well overall this is what I do known.
1) 5th Connecticut lost their National Flag (Regimental saved)
2) 28th New York lost their Regimental Flag (Maybe the National flag was the third flag?)
Here is a website with the 28th NY's "Regimental Flag" although it looks like a National Flag.
http://www.28thnycoe.com/articles/07Feb-flag.htm
Maybe it could have been a flag from another regiment. 46th PA?
Well don't know
Have a good day,
Shawn Prouty