Hello Jim,
A unit the size of a battalion would indeed need a flag to perform its maneuvers with - so they would indeed have been issued such a flag.
In the French Army of the Napoleonic Wars regiments were much bigger than Civil War regiments, and they would have from 2-4 maneuver battalions. Each had its own flag.
I know that Confederate battalions, units raised as such, were all issued with flags.
Greg Biggs