Ken,
I find nothing that would indicate the 9th Alabama
lost a flag at Sharpsburg. However, three Color Bearers were reported wounded.
The 35th NY is credited with taking at least two flags at that engagement;
WD#81, a third ANV pattern (MOC) with tentative
ID as 1st Louisiana Inf.
A 15 star first national housed at the NYSM Museum, with tentative ID as "Alabama" Regiment.

What is the source for the statement you quote?

Ken Legendre