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If you have one of the native hardware Black Magic Probes the process of upgrading the firmware is as follows:
Linux / MacOS
Download or compile a Black Magic Probe (BMP) firmware.
Plug in the Black Magic Probe into your computer and run the following command:
sudo dfu-util -d 1d50:6018,:6017 -s 0x08002000:leave -D blackmagic.bin
If this does not manage to switch your BMP into bootloader mode you can also plug in your BMP while holding down the button. This will force the BMP to stay in the bootloader on power up.
You can use the Upgrade.exe program.