Two lists of captured flags are to be found in the Mobile Campaign reports. The first (OR 49/1 p 103) states that 5 flags were taken at Blakely by the 97th Ill, 119th Ill, 8th Ill, 83rd Oh, and 119th Ill; 2 flags were captured at Blakely Fort by 119th Ill and 122nd Ill; 1 flag was captured near Blakey Fort by the 1st La; and 1 flag was taken at Spanish Fort by the 8th Ia. Furthermore "Three flags were found by mean of the Third Division, Sixteenth Army Corps, after the capture of of Spanish Fort". Finally it states that "Two other flags captured by General Lucas' command in the operations about Mobile have not been received" This list then accounts for 14 flags.
The second list (OR 49/1 p 313) provides the names of 11 men that received the Medal of Honor for capturing a flag. It includes the first 9 flags listed above and then includes 2 additional flags, one taken by the 97th Ill at Blakely on April 9 and the other captured by the 1st La at Mount Pleasant on April 11. If these are separate flags that increases the total number listed to 16.
However, note that these lists only provide for 2 flags captured by the 97th Ill whereas their Colonel clearly mentions 3 of them. Again. if the two lists are not duplicating flag captures the total now is 17 flags.