I do know that many of the Captains and crews who were Southern sympathizers took their boats to different rivers in the South to avoid them being captured by Federals. Martial law in Missouri required that the captain and crew members of any boat operating on the Missouri during the war take a loyalty oath, and in some cases, post a substantial bond. At one point, I believe it was Frank Blair who completely closed the Missouri River to steamboat traffic. I've read a number of stories about boats being captured and used by opposing forces, as well as some that were destroyed.
In the "Border War" days, the Emigrant Aid Societies of the N.E. sent "settlers" (on their way to Kansas Territory) up the Missouri on steamboats. In fact, at least one such boat was forced to turn around and take its passengers back to St. Louis. Another time, a boat was boarded by "ruffians" at Lexington. Part of the cargo was in boxes labeled "BIBLES", but when the boxes were opened, they were found to contain rifles. A preacher by the name of Beecher was responsible for the shipment, thus the rifles became known as "Beecher's Bibles".
Thanks again for the good tips on more info.
Best regards,
Maggie