While I agree with Greg that WD#331 is NOT the HQ flag of Custis Lee.
I must take issue with the statement that most of these HQ flags would
have been 2nd or 3rd nationals.
There was by no means any set or regulation way of designating a General's
HQ.
Of the surviving identified HQ flags associated with the Army of Northern
Virginia I found 5 first nationals, 9 ANV pattern Battleflags, 8 second nationals,
5 flags of special design, and only one third national and that is suspected as
being post-war. These tabulations do not include the silk battleflags that the
Cary cousins presented to Generals Beauregard, Johnston, and Van Dorn in Dec. 1861.
While the five "special" designation flags would seem to indicate a system of marking
the HQ's of different commanders; no such order or documentation has been found to support
that theory.

Ken Legendre