The flag you are speaking of (an 11 star 1st National) is shown in Glenn Dedmondts book "The Flag of Civil War Arkansas".
I still do not understand why they would have left it behind in the luggage at Aquia Creek. I know that the Battalion was ordered to only carry their light marching order of only 35 pounds. Wagons were supposed to come for the tentage and trunks but did not get them before the Yankee landed and raided the abandoned camp. But why would they leave a National Flag unless they had been issued a newer set of National and Regimental flags? It was about that time (March 1862) that the Virginia Battle Flags were being issued. But wouldn't they have kept using their National Flag also?
Also it seems that the 2nd AR. Batt. was engaged in the trenches at Yorktown and the retreat to Williamsburg under Joe Johnson before being assigned to Pettigrew and being involved in the Battle of Seven Pines. So the 2nd Ar. Batt. battle honors would have been Aquia Creek, Yorktown, Williamsburg, Seven Pines, and finally Mechanicsburg.