Dex,
It's going to be really tough to chase down without knowing what boat he might have been associated with, and which rivers he was operating on. One might assume he was on the Mississippi because of where he lived. If he left for the South, it was probably because he wasn't about to take the loyalty oath that was required of all steamboat personnel that were operating out of St. Louis. Such was the case with many Captains and boat owners on both the Missouri and Mississippi Rivers. Many took their boats to Southern rivers to avoid them being pressed into Union service or confiscated or destroyed.

One of my best sources for obscure information has been old newspaper archives from the time period. It would be a long-shot, but if you can find archives from a local paper, there might be some mention of the Captain & daughter leaving.

I wish you much luck in your quest.
"steamboat granny"
Maggie Gilbert