Both Flags captured by Tom Custer are accounted for.
Both are at the MOC
WD#325 taken at Sailor's Creek (2nd Va Reserves)
WD#304 taken at Nazomine Church (2nd NC Cav)

The Virginia State flag at the Appomattox NPS did indeed
come to that Park as a loan from the Custer Battlefield NPS.
One can only guess as to how and when that flag came into
Custer's possession.
Given the pre-war design of the Virginia State Seal; it was probably
stolen from some home.
Incidently, the reverse side of the Flag bears a portrait of George Washington.

Also George Custer makes a claim of "capturing" a Virginia Flag at Williamsburg.
Perhaps the Flag came from there or Yorktown.

Ken Legendre