I think most of the flags were given to the State after the war ended and are at the Missouri State Museum (at the Capitol). Only a few of the flags have been restored. If I recollect correctly, most are still rolled-up and in glass boxes. I know the 9th MSM Cav flag was borrowed from the Museum around 1900 for a reunion and I assume returned. I have not found anything specific in regard to that flag as to its current status. I think only one MSM flag has been restored.

Go here for some information about the flags at the museum:
http://www.sos.mo.gov/archives/mdh_splash/default.asp?coll=cwflag