I know the 1st Michigan infantry had lost a flag. I am not sure if they lost two or more, but so far I have found only one flag captured. The 1st Michigan went the farthest at 1st Manassas.
The flag captured was a regimental flag. The flag was returned in 1886.
I do have a picture of the flag, I found all Michigan flags on a website back on May 24th, 2001.
I found the site, not only does it have infantry, but artillery, sharpshooters etc.
Have a great day,