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It seems, due SAM-BA (SAM Boot Assistant) inside ATSAM3X8E being listening to both Native USB and UART USB ports after a Reset for programming, allowing talking with SAM-BA, this time from your PC, through BOSSA (bossac.exe, Basic Open Source Sam boot Assistant), then it would make not possible to program an Arduino Due while having both USB port connected to a PC.

Can somebody confirm, this is the reason?

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    Do you get a particular error when you try this?
    – PMF
    Jun 11 at 6:23
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It should be possible to do because when you flash the microcontroller needs to be in the flashing mode that only works with the Native port, to enable that mode you have to press the erase button for around 2 seconds and then press Reset...

I made a guide on how to do this here

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