It also might not be a big deal if you do fairly benign things that don't necessitate a hard reset while the USB is in use. At the very least, you might try to advise users to close the Arduino Serial Monitor or any program accessing the native port before pressing that button!
Thank you Paul that is good to know. I assume users would occasionally run into this. They would be using it primarily to load new sketches, but I'm sure many would also use the virtual serial port to monitor and/or debug. There's no reason however that I'd expect the device to hard reset during operation, except as needed when loading a new sketch. In this case, the user wouldn't un-plug and re-plug the USB cable (I wouldn't expect anyway).
Does that still sound like a serious problem, or are you referring primarily to the situation where the user has the virtual serial port in operation and the SAM3X is suddenly reset?
I've never personally experienced this, and I've been using the Due with Windows 7 for a while now, but I also do not use the virtual serial port much. Interesting side note that getting my Windows 7 machine and the Arduino IDE to play nicely with the 16U2 was a real hassle. It was happy to work with the native USB port on the SAM3X right away though. I found other posts here on the forum about the same problems I was having.
Thank you again for the guidance on this.
Anyone else have any thoughts? Can anyone confirm that the Arduino IDE should work right out of the box with a blank SAM3X chip connecting to the native USB port?