The 46th Pennsylvania lost their State Flag on May 2nd, 1863. It did not mention anymore details. If this is true then clearly the 12th Corps indeed lost a flag during the Civil War.
The 46th Pennsylvania was in Knipe's Brigade, William's Division, 12th Corps.
46th Pennsylvania losses at Chancellorsville:
81 Captured (Most likely along with the State Flag)
Have a good night,