We do this all the time. We have many variables that we can adjust all the time.
you can see the code as part of our 2010 code.
http://www.frc272.com/seminar/Archive/.
We call the LCConfig.cpp. You can change the config file, save it via FTP to the Crio, press a button and have it read in to the running code then have it apply the new settings. Once you like them leave it there. The config is read in when we boot up. Very flexible.