In first Mi5 release for nougat, ingzbry wrote 'never wipe /system partition manually in your life', see
https://xiaomi.eu/community/threads/6-12-8.36620/
I'd ask him directly on our to workaround the issue . Situation happened to me on a mi4, was not holding fastboot anymore
but it worked with engineering cable (important thing I remind I unpluged the battery to flash phone)
again, strange that with engineering cable QC drivers do not show up on your PC, can you try unplugging your battery with engi cable ?