Five hundred forty five captured Confederate flags were sent to the US War Dept after the War Between the States ended, and the government began cataloging them with plans to return them to their states of origin, according to an article in the UDC magazine, November 2011.
These were finally returned in 1905 while Taft was Secretary of War. Thirteen of the flags were returned to Alabama. Many others flags still remained in the hands of Northern captors and some had been carried home by Confederate soldiers and flag bearers for safekeeping.
Over the past one hundred and fifty years, flags have been found in trunks, drawers, attics and basements, of houses, courthouses, state buildings, and in almost any place one could imagine. Many have found their way to the Alabama Department of Archives and History where some have been conserved. Their flag collection consists of ninety period flags.About seventy are still in need of conservation, according to the article.