I have found information about the 39th Iowa in my wait for a response from the Minnesota Historical Society. According to the website posted below, at the battle of Allatoona Pass the national flag of the 39th Iowa was captured in bitter hand to hand combat. Don Troiani painted a scene from that fight and notes the incident of its capture.

http://www.civilwarvirtualtours.com/allatoonapass/1040am.html