Só para nunca mais ter que procurar isto, o que é recorrente de x em x meses dado que o flash-all.bat falha:
Step 7: If your bootloader is already unlocked, skip this step. If it is not, it has to be unlocked in order to flash anything. To do this, use the command:
Use the Vol Up to go up to yes and then use the power key to select. The device should now be unlocked
Step 8: We now want to wipe the device. Use the following commands in order:
Step 9: We will now flash the bootloader. It is important that you do not disconnect the device or mess with it during this step or else you hard brick the device.
Step 10: If using a phone or data enabled tablet, we will now flash the mobile radios. Some phones have more than one radio file. Flash the CDMA radio after the LTE radio.
Step 11: We will now flash the system, boot, and recovery all in one shot with the following command:
Alternatively, you could extract all the .img files in the zip file and flash them manually one at a time. This makes things really handy if you’re using the factory image to act as an update rather than a complete return to stock. If trying to update using the factory image, extract the .img from the zip file into the same directory as your bootloader and radio img files and execute the following commands in order:
If going for a complete back to stock using the manual flashing of the zip file, execute the following commands after the above 4:
Step 12: The device now has been flash back to stock. Only one thing left to do is reboot.
Your device will now reboot and should be completely back to stock as well as be unrooted.
Source e crédito do tutorial: http://androidforums.com/threads/guide-how-to-flash-a-nexus-factory-image-manually.706533/