While doing a little experiment with the Atmel XMEGA-A3BU Xplained kit, I ran into a few little hiccups. I wanted to document the steps that I took to get things going.
1. When you power up the board via the mini USB cable, it will default to running the application. The USB port will be configured for virtual COM operation, but the driver must be installed: download the .inf file from the A3BUXPLAINED page. Then, go into Device Manager to update the unknown CDC port using that .inf file.
2. If you hold down SW0 when you power up, the board will enter the DFU bootloader mode. The USB port will be configured for the DFU bootloader service, but the driver must be installed: download the FLIP software from the FLIP page. Then, go into Device Manager to update the driver for the DFU ATXMEGA256A3BU / ATxmega256A3BU device. Point to the /usb subdirectory in the FLIP installation directory.
3. To reinstall the original Xplained demos program, start Atmel Studio (available here) and select "New Example Project...", from the start page. Navigate the tree [Atmel]+[Atmel Corp. - ASF (3.9.1.)]+[XMEGA-A3BU-Xplained]+[XMEGA-A3BU Xplained demo application] to open the project for the demo program. Build the project to create the .hex file in the output directory. Then load the board via the FLIP utility.
4. By default the FLIP utility will scan the first 20 (or so - I forget exactly) COM ports. My system has been enumerating so many FTDI virtual com ports that I'm now up to COM42. You may need to adjust the preferences to raise the number of COM ports being scanned.