Here are the questions (consider I'll be using a USBasp, and I'll edit the avrdude.conf for the proper signature of my Atmega328 non-P):
Q1) the Atmega328 I'll be using as the "rescuer" chip already has the Arduino bootloader (Uno) flashed to it, and is already configured to use the external 16MHz crystal. When I am to flash the new fuses to this chip, should I have it in an arduino board with the crystal or in a breadboard without any crystal?
Q2) How do I flash the BIN file? (I know how to flash the HEX file).
.bin files are programmed to EEPROM with avrdude the same way (almost) that .hex files are programmed to the flash.
Avrdude should auto-detect the .bin format, so:
a[color=brown]vrdude -patmega328p -carduino -P /dev/tty.usbmodemfd3141 -U eeprom:w:/Downloads/atmega_fusebit_doctor_2.11_m328p.bin[/color]
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.00s
avrdude: Device signature = 0x1e950f
avrdude: reading input file "/Downloads/atmega_fusebit_doctor_2.11_m328p.bin"
avrdude: input file /Downloads/atmega_fusebit_doctor_2.11_m328p.bin auto detected as raw binary
avrdude: writing eeprom (1024 bytes):