Burn bootloader to 32u4 fails

[Smashcat]

This has been an issue for a few years now. The Arduino IDE (currently using 2.2.0) cannot burn the bootloader to this chip as it attempts to set the high fuse bits, which cannot be done. Unsure why this still isn't fixed. Typical error message:

avrdude: WARNING: invalid value for unused bits in fuse "lock", should be set to 1 according to datasheet
This behaviour is deprecated and will result in an error in future version
You probably want to use 0xff instead of 0x3f (double check with your datasheet first).
avrdude: verification error, first mismatch at byte 0x0000
0xf3 != 0xcb
avrdude: verification error; content mismatch
Failed chip erase: uploading error: exit status 1

[Smashcat]

This is using an ATMEL ICE programmer to a 32u4 on a custom board. The chip can be programmed/tested using the Microchip Studio IDE, and it does appear as a USB device also, so that part is working.