I found a site that tells the story of the 31st Missouri flags that were saved.
Go to Google,
Type in "flags captured at Chickasaw Bayou"
Search for "Military History and Reminiscences of the Thirteenth Regiment of Illinois".
Scroll down to page 283.
It won't let me send the web page link for some crazy reason. This proves that the 31st Missouri flags (National and State) were saved. This is the same story I have always known of the battle.