I spent now hours on the internet (btw. after Microchip took over, the support sites are a mess, most ATMEL links do not work anymore), but I could not solve my issue yet and getting really frustrated.
I have an AT32UC3A3256 (in 144 TQFP package) and thought that I can program it without any external programmer due to the preinstalled bootloader. When I powered my custom made board and made the USB connection the MCU was never detected and enumerated. And then the disaster began. After fiddling around with Windows and Linux Ubuntu without having success I thought let's program my software directly. Thus, I connected my JTAGICE3 and flashed the memory. Unfortunately I killed the bootloader by this and of course I had no success getting the MCU being enumerated by the USB host. Getting back the bootloader with Atmel Studio 7 seems not possible because I couldn't find it, the Atmel docs always forward me to avr32studio, but this old IDE does not support the JTAGICE3, the avr32 toolchain 2.4 neither and so on and nowhere a binary bootloader file was available. So finally have spent my whole Saturday for nothing. At the end I found here somebody who has posted the binary of the bootloader. I programmed this with Studio 7 (because that is the only tool I can use with JTAGICE3) but back at the previous situation: The device is not detected by the host, regardless what you do. And, what is also strange: The MCU should run on a 12MHz crystal connected to pin 18/19. So I expect to see 12MHz there, but I can only see 55kHz there with my scope regardless what I do. Of course I can not longer guarantee that the bootloader is working fine.
Any idea what to do now? Any help is welcome.