Robert,
I'm really curious now. You have ancestors who lived in Indian Territory before the war but were in Missouri in 1865?

Here's some theories for you to disprove (or ignore!): They moved to Missouri because it was safer in 1865 whether or not you were pro-Union. They moved to Missouri because they were Southern Cherokee and could not safely return to the Nation and/or their property was taken by 'Loyal Cherokee'. Or, they were Cherokee living in Missouri before the war for economic reasons or because they were Treaty Party and considered the Nation unsafe.

Just some unsolicited thoughts.