My guess is Phi Psi house in Lawrence. For decades they bragged they had the world's largest Confederate flag, which they periodically hung over the front of their house. I went to grad school with a member at KU, and while he put heavy starch in his underwear, he often bragged about their "collection of flags".
Flag theft is probably due to a dream pledge prank. APO flag probably lies someplace we would not expect.
Spoken like a true low rent Yankee or history revisionist. The Confederate flag is the last true flag of the constitution that gave states rights.