Actually, there were two color bearers, the national color bearer and the regimental color bearer. Niether account designates which color was captured, neither the federal account or confederate.

Thus, while - lets say - the national colors (or american flag) was captured, the regimental colors (which were blue and usually decorated with a state seal and regimental designation) made it safely back to friendly lines.

The Confederate account implies that the capture"r" ran forward to retrieve fallen colors that were aparently abandoned on the field of battle, while the Federal account implies that one of the bearers, although mortally wounded - bore HIS flag back to the safety of his comrades.