Do this:
File > Preferences
Check the box next to "Show verbose output during: upload".
Click the "OK" button.
Upload a sketch to your Arduino board.
After the upload finishes, examine the contents of the black console window at the bottom of the Arduino IDE window. You will need to scroll up to see it all. There you will find the upload command the Arduino IDE generated. It might look something like this:
C:\Users\per\AppData\Local\Arduino15\packages\arduino\tools\bossac\1.7.0-arduino3/bossac.exe -i -d --port=COM11 -U true -i -e -w -v C:\Users\per\AppData\Local\Temp\arduino_build_693683/Blink.ino.bin -R
Copy and paste that command to a text editor. Change the filename of the .bin file to the file you want to upload. If the paths contain spaces, wrap them in quotes.
Press release the reset button on your Arduino board quickly twice. You should now see the onboard LED pulsing to indicate it's in bootloader mode.
Open a command prompt.
Run the modified command from the command prompt. The .bin file should be successfully uploaded.