Here's some background that may be of use. Generally speaking, there was no specific directive governing captured battle flags. In most cases, the flags were passed up through the chain of command, sometimes with a note explaining date and place of capture; sometimes not. In some cases, the captors kept the flags as souvenirs. Those flags that were sent up the chain eventually ended up at the Adjutant General's office in D.C. - about 500 of them. In 1905, the USG sent all the flags back to the governors of each former Confederate state. Those that couldn't be associated with a particular unit ended were given to the Confederate Memorial Association in Richmond.
Before returning the flags, the AGs office developed an inventory of each flag with as much information as they could determine. Two of the flags listed in the inventory are flags captured at Phillipi.
#29: Confederate Flag, Stars and Bars, captured at Phillipi, Virginia, June 3rd 1861 by Lieut. Wm. B. McCartney, Co. B 16th Regiment Ohio Volunteers. Returned 3/25/05 to Virginia.
#84: Virginia State Flag captured at Battle of Philippi Va. June 3rd 1861 by the 14th Regiment Ohio Volunteers. Inscribed: Presented by the Ladies of Bath Va. Motto: God Protect the Right.
There is no listing for a third flag, but that doesn't mean anything. BTW, all of this information is taken from The Returned Battle Flags, Richard Rollins, ed. (Redondo beach, CA: Rank and File Publications, 1995).