In the early days of the war company flags could be, and were, still used in battle. Also consider that since it was found in the fort that it might have been aprt of any unit baggage left behind when the Confederates elft it.

For example, the 15th Mississippi lost at least 7 flags at Mill Springs, KY in January, 1862 - one takn in battle (maybe two) and the rest from their pilferred camp site.

While company flags were intended to be sent home of stored in baggae, they still managed to find their way to the battle flines during the war, even as late as 1865.

Greg Biggs