We put together a ChipworkX updater application. It will erase the device then update TinyBooter and Firmware from the SDK.
So when the firmware needs to be updated, just run this application. No need for a command prompt or MFDeploy.
Hopefully, this will make things easier.
The ChipworkXUpdater.exe is now part of the GHI NETMF and .NET Gadgeteer package. Which is #3 under system preparation.
This is now part of the SDK