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Seems to me that byte blaster all have the same USB serial number, so Windows can't work out which one is which.
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No,no.
Generally, USB devices don't need individual serial numbers to be distinguished by the Windows OS or the application software. They are also enumerated by connected interface and possibly involved hub ports. Of course, there's sometimes a problem in identifying the individual adapters, at worst case, USB-0 and USB-1 (as they are named by the Quartus JTAG driver stack) can change their places in some situation. But they are, at least in the Quartus tools, individually accesible. There may be a flaw with the NIOS II tools, as said, I don't know about.
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