I have a numebr of period newspaper articles, North and South, regarding black flags - and have doubts as to how many actually existed! One of my favorites, and this one did exist, was for the Mobile Bay Chasseurs which carried a black flag trimmed in red fringe and had a reg gallows embroidered on it with the slogan "Lincoln Avenue South" and the unit name on the other side!!!! They were Alabama militia.
As for Union flags - Shawn - seek out a copy of the small book by Malcolm R. Smith called "Flags of the Confederacy" because therein he reprints a copy of the House of Representatives February 16, 1888 report on captured flags and the list includes a LOT of Union flags!!! This was a letter from the then Secretary of War William Endicott. Exhibit H of the document lists the Union flags.