Complex sentence: Canby in Shreveport, Louisiana, then took custody of Smith's force of 43,000 soldiers when they surrendered, by then the only significant Confederate forces left west of the Mississippi River.
Split into simpler sentences: Canby in Shreveport, Louisiana, then took custody of Smith's force of 43,000 soldiers when they surrendered. Gen. Smith surrendered his troops which by then was the only significant Confederate forces left west of the Mississippi River.