A patch https://patchwork.kernel.org/patch/10212201/ is going to fix
this issue properly, it should be backported to older kernels too, so
hopefully going forward your NVMe drives won't require any workarounds,
it should also fix USB-C detection too

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  NVME devices and Network devices disappears upon suspend

Status in linux package in Ubuntu:
Status in linux source package in Yakkety:
  Won't Fix

Bug description:
  Ubuntu 16.10 on a Alienware 15 R2 when resuming from suspend the NVME
  devices and network devices are gone.

  I can force the devices to re-appear issuing echo 1 >
  /sys/bus/pci/rescan, that was what I did to be able to submit this bug
  report from a live USB stick.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.10
  Package: linux-image-4.8.0-22-generic 4.8.0-22.24
  ProcVersionSignature: Ubuntu 4.8.0-22.24-generic 4.8.0
  Uname: Linux 4.8.0-22-generic x86_64
  ApportVersion: 2.20.3-0ubuntu8
  Architecture: amd64
  CasperVersion: 1.379
  CurrentDesktop: Unity
  Date: Mon Jan  9 17:55:50 2017
  LiveMediaBuild: Ubuntu 16.10 "Yakkety Yak" - Release amd64 (20161012.2)
  MachineType: Alienware Alienware 15 R2
   PATH=(custom, no user)
  ProcFB: 0 inteldrmfb
  ProcKernelCmdLine: BOOT_IMAGE=/casper/vmlinuz.efi 
file=/cdrom/preseed/hostname.seed boot=casper quiet splash ---
  PulseList: Error: command ['pacmd', 'list'] failed with exit code 1: No 
PulseAudio daemon running, or not running as session daemon.
   linux-restricted-modules-4.8.0-22-generic N/A
   linux-backports-modules-4.8.0-22-generic  N/A
   linux-firmware                            1.161
  SourcePackage: linux
  UpgradeStatus: No upgrade log present (probably fresh install)
  dmi.bios.date: 09/30/2016
  dmi.bios.vendor: Alienware
  dmi.bios.version: 1.3.9
  dmi.board.name: 0X70NC
  dmi.board.vendor: Alienware
  dmi.board.version: A00
  dmi.chassis.type: 10
  dmi.chassis.vendor: Alienware
  dmi.chassis.version: Not Specified
  dmi.product.name: Alienware 15 R2
  dmi.product.version: 1.3.9
  dmi.sys.vendor: Alienware

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