I was investigating update_scripts failures as part of  bug 674759  and I noticed that this vm was high on the list. I took a look and saw that it was failing with

Aborting
could not detach HEAD
Failed to update depot_tools.
Looking for .gclient starting from E:\b\build

Traceback (most recent call last):
  File "E:\b\depot_tools\gclient.py", line 2146, in <module>
    sys.exit(main(sys.argv[1:]))
  File "E:\b\depot_tools\gclient.py", line 2132, in main
    return dispatcher.execute(OptionParser(), argv)
  File "E:\b\depot_tools\subcommand.py", line 252, in execute
    return command(parser, args[1:])
  File "E:\b\depot_tools\gclient.py", line 1883, in CMDsync
    client = GClient.LoadCurrentConfig(options)
  File "E:\b\depot_tools\gclient.py", line 1250, in LoadCurrentConfig
    path = gclient_utils.FindGclientRoot(os.getcwd(), options.config_filename)
  File "E:\b\depot_tools\gclient_utils.py", line 608, in FindGclientRoot
    exec(FileRead(entries_filename), scope)
TypeError: expected string without null bytes

Hopping on the machine, I found that the .gclient_entries file was completely full of null bytes. I deleted that file and sync'd again and it complains now that the .git/index file is corrupted (it's also completely full on null bytes). I suspect a crash on the VM may have committed journaled metadata but not actually the data for these and possibly other files. I would suspect the integrity of the entire VM.