Terry,
The Waggeman source comes from the SHSP.
He basically stated that before the flag was surrendered he was allowed to cut approximately
a 10" piece off of the fly end from top to bottom
to include the fly-most stars. I have inspected all
the Appomattox surrendered flags looking for a flag
that was missing a part of the fly that would fit the
Waggeman piece. Found none that did so. Perhaps, following Waggeman's example, the rest of
the flag was also cut into pieces.
It was not at all uncommon for the units to cut their
flags in pieces rather than surrender them. Some
were burned. I have found dozens of sources that
state this was done.
No doubt, the Federals also helped themselves to
souvenirs.

Ken