Let's clear the air with the terminology - VO = FA
Once you've loaded the VO into the car, you have not VO coded any modules. In order to VO code modules, you either have the modified VO saved into the VCM or you can work off the modified VO file.
To VO code the ECU you want changed, click on the ECU in the SVT Tree such as Fembody and click CODE. This will code the ECU based on the VO loaded either in your car or in E-Sys. Course after that you'll have to make your FDL coding changes again.
Hope that helps!
And of course, DO NOT click CODE DEFAULT. That will just screw you but I'm sure you know.