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blink1-tool and serial number
Option -d or --id won't work with serial when the serial number is not one of a known mk2. I use my own serial (as it is open hardware I made my own boards) so I cannot use blink1-tool. I will have to use serial from your boards ...
Please give more details. There is nothing in blink1-tool that restricts which serial numbers to use. The only restrictions are the serial number must be in the USB device descriptor and it must be a 4-byte hex string (e.g. "ABCD1234" is valid but "JKLMZXCV" is not valid)
Also, do you have a link to your board firmware and design files? Perhaps there's an issue with your firmware I can help with.
OK so here is my HW design : circuitMaker I only changed the LED because I did not found the other but it has the same driver.
The firmware is your hex not even recompiled
I used serial reference
If I use the serial 0x01000000 (I noticed you used big endian it may not be best choise because Microchip MPLAB X IPE can be used to generate serials but in little endian. But I respect and this choice and have no problem with it). So with this serial the --list won't show (mk2) AND -d 0x01000000 won't work.
I solved the problem using same serial as reserved for seeedstudio Q1 2017 (I made my PCB there too ;) but I do not find this very clean. Note also I do not plan to sell this boards (at least not more than a few units) so this serial problem is not crytical.