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Debug Select set to GPIO is used to repurpose the SWD pins. You will still be able to acquire the device.
Chip protection is used to block access to the device. When the Chip Protection is set to Protected, you will not be able to access the device until you do a complete erase. You cannot read from the device as well.
When the Chip Protection is set to Kill mode, any access to the device is blocked and even the flash erase will not work. You can refer to the Architecture TRM for information regarding this.
Also when working with a bootloader, the Flash Protection does nothing but prevent the BL from overwriting itself, correct?
Yes, that is correct. It is used to prevent the bootloader code from being modified in any way. It includes protection from any malicious code or the user application accidentally writing to the bootloader region.
You can refer to this KBA for write protecting bootloader code - Bootloader Host Error: “The Flash Row is not Valid for the Selected Array” - KBA221445
Thanks and Regards,
Rakshith M B