If I may, I would like to add to this. Confederate units usually only carried one flag unlike federal units that generally carried two (federal & state) Confederate forces carried a wide variety of colours that ranged from original designs to State or Confederate "National" flags with unit designations and of course the "Battle flag". The Confederate flag known as the "Battle flag" is the one which incorporates the cross of St. Andrews on the entire flag. ALL flags carried by Southern troops on the field were flags of Battle. Many states when they seceeded changed their flag to reflect their secesion. I find it amusing living here in Virginia when people raise a fuss over the Battleflag. The flag of the Commowealth of Va. still reflects the changes made to it when it seceeded and therefore is still a Confederate battleflag. SHHHHH. dont tell anyone cause they'ld probably want to do like Georgia and change it. So, to make a short story long; yes, all flags were ordered to be turned over when the unit surrendered. Many; as Reb has said were torn up and the pcs. given out to the remaining soldiers rather than be turned over to the Federals. Many of the flags in museums have large pcs. cut from them for the same reason. I have read a few accounts were many old veterans were buried with their "piece of the colours".