I had no idea how to proceed either.
Since @jmaxou sugested that we could edit the source code, and I couldnt see 
where this source were, I assumed it could be get from the .deb file.
I searched how to do it from the deb package. Turned out its like a zip, we can 
extract its contents.
I got the last deb package, the one built to kernel 4.8, depacked, edited and 
repacked.
this site shows how to do it
https://unix.stackexchange.com/questions/138188/easily-unpack-deb-edit-postinst-and-repack-deb
actually is pretty simple.
If I understood well, it should be packed using the kernel you want to target. 
But I can be wrong in this point
Sorry if I cant be of more help, first time doing it as well.
Anyway, anybody knows how can we make those fixes to be part of ubuntu itself?
Tired of the bluetooth not working each update
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https://bugs.launchpad.net/bugs/1542743

Title:
  Bluetooth: Patch file not found ar3k/AthrBT_0x00000200.dfu

Status in bluez package in Ubuntu:
  Confirmed

Bug description:
  Since some Versions of Linux Kernel and Ubuntu Releases this problem
  exists.

  I am now running ubuntu 16.04 prerelease and still have the same
  problem.

  Bluetooth does not work with the atheros device on  msi gt 72 2qd
  notebook.

  WORKAROUND FOR [0CF3:3004] DEVICE ONLY with kernel 4.4:

  sudo apt install dkms
  wget 
https://launchpad.net/~hanipouspilot/+archive/ubuntu/bluetooth/+files/btusb-lp1542743-dkms_0.1_all.deb
  sudo dpkg -i btusb-lp1542743-dkms_0.1_all.deb

  FOR KERNEL 4.8 A WORKAROUND DKMS DEB IS

  https://launchpad.net/~hanipouspilot/+archive/ubuntu/bluetooth/+files
  /btusb-lp1542743-dkms_0.2~4.8_all.deb

  dmesg | grep Bluetooth:
  [    2.655360] Bluetooth: Core ver 2.21
  [    2.655373] Bluetooth: HCI device and connection manager initialized
  [    2.655377] Bluetooth: HCI socket layer initialized
  [    2.655379] Bluetooth: L2CAP socket layer initialized
  [    2.655385] Bluetooth: SCO socket layer initialized
  [    6.612790] Bluetooth: BNEP (Ethernet Emulation) ver 1.3
  [    6.612794] Bluetooth: BNEP filters: protocol multicast
  [    6.612798] Bluetooth: BNEP socket layer initialized
  [    9.016880] Bluetooth: Patch file not found ar3k/AthrBT_0x00000200.dfu
  [    9.016882] Bluetooth: Loading patch file failed

  hwinfo | grep Bluetooth:
  <6>[    6.612790] Bluetooth: BNEP (Ethernet Emulation) ver 1.3
    <6>[    6.612794] Bluetooth: BNEP filters: protocol multicast
    <6>[    6.612798] Bluetooth: BNEP socket layer initialized
    <3>[    9.016880] Bluetooth: Patch file not found ar3k/AthrBT_0x00000200.dfu
    <3>[    9.016882] Bluetooth: Loading patch file failed
  60: USB 00.0: 11500 Bluetooth Device
    Model: "Atheros AR3012 Bluetooth 4.0"
    Device: usb 0x3004 "AR3012 Bluetooth 4.0"

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: bluez 5.36-0ubuntu1
  ProcVersionSignature: Ubuntu 4.4.0-2.16-generic 4.4.0
  Uname: Linux 4.4.0-2-generic x86_64
  NonfreeKernelModules: nvidia_uvm nvidia
  ApportVersion: 2.19.4-0ubuntu2
  Architecture: amd64
  Date: Sun Feb  7 00:38:04 2016
  ExecutablePath: /usr/lib/bluetooth/bluetoothd
  InstallationDate: Installed on 2015-10-24 (105 days ago)
  InstallationMedia: Ubuntu 15.10 "Wily Werewolf" - Release amd64 (20151021)
  InterestingModules: bnep btusb bluetooth
  MachineType: Micro-Star International Co., Ltd. GT72 2QD
  ProcEnviron:
   LANG=de_DE.UTF-8
   PATH=(custom, no user)
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.4.0-2-generic 
root=UUID=f7880b23-39b5-423a-bdbf-62b111783450 ro quiet splash
  SourcePackage: bluez
  UpgradeStatus: Upgraded to xenial on 2016-02-02 (4 days ago)
  dmi.bios.date: 12/19/2014
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: E1781IMS.10I
  dmi.board.asset.tag: To be filled by O.E.M.
  dmi.board.name: MS-1781
  dmi.board.vendor: Micro-Star International Co., Ltd.
  dmi.board.version: REV:0.C
  dmi.chassis.asset.tag: To Be Filled By O.E.M.
  dmi.chassis.type: 10
  dmi.chassis.vendor: Micro-Star International Co., Ltd.
  dmi.chassis.version: To Be Filled By O.E.M.
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvrE1781IMS.10I:bd12/19/2014:svnMicro-StarInternationalCo.,Ltd.:pnGT722QD:pvrREV0.C:rvnMicro-StarInternationalCo.,Ltd.:rnMS-1781:rvrREV0.C:cvnMicro-StarInternationalCo.,Ltd.:ct10:cvrToBeFilledByO.E.M.:
  dmi.product.name: GT72 2QD
  dmi.product.version: REV:0.C
  dmi.sys.vendor: Micro-Star International Co., Ltd.
  hciconfig:

  rfkill:
   0: phy0: Wireless LAN
    Soft blocked: yes
    Hard blocked: no

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