It sounds from your post, right clicking on your Planned RX rate Job/map and selecting Workorder/console, has been completed correctly. If you open Windows Explore and locate your drive reading the USB you should be seeing a Folder called AgGPS, (Data folder) where all the Client/Farm/Field information will be saved. There will also be a folder called Presecriptions, where the Planned workorders are exported to.
One thing to try is manually cutting/pasting the previous folders on the USB to another location on your computer BEFORE - completing the Write Job Data. When you Browse for the location, only select Drive reading USB. Be very careful to never place an AgGPS folder within another AgGPS folder.
You should contact your Trimble Dealer on how to remove that data from the FmX. I was certain that during the Tranfer of files from USB to FmX, there was an option to select to replace existing data on FmX with data on the USB.