There is functionality in the Smart Device Framework that will allow you to change the timezone programmatically on the device. Unfortunately, there's nothing built directly into RAPI that will allow you to do the same remotely, but fear not as you still have a couple of options:
1. Write a RAPI Extension library.
If you're comfortable with native code, you can create a set of RAPI Extension methods that you can call via RAPI::Invoke().
2. The Client/Server Way.
Create an app that will open a socket and listen on a specific port on the device. When the device is connected via ActiveSync/WMDC, you can connect to the open socket from the desktop and send commands to the device. Define a simple protocol that will allow you to adjust the timezone and date/time settings on the device. You can use RAPI to deploy, launch and terminate the app on the device.