I just found related bug here: 
https://bugs.launchpad.net/ubuntu/+source/firefox/+bug/999110
SO this can be closed or linked to the previous.

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You received this bug notification because you are a member of Desktop
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https://bugs.launchpad.net/bugs/1663007

Title:
  Bookmarks are gone and cannot be restored from backups or even from
  html file.

Status in firefox package in Ubuntu:
  New

Bug description:
  After I restarted my firefox, all Bookmarks has gone. 
  Just before restart - there was a problem with firefox sync. I have logged 
in, but it had old bookmarks. Then I restarted and all bookmarks were gone and 
I cannot get them back.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: firefox 51.0.1+build2-0ubuntu0.16.04.2
  ProcVersionSignature: Ubuntu 4.4.0-62.83-generic 4.4.40
  Uname: Linux 4.4.0-62-generic x86_64
  AddonCompatCheckDisabled: False
  ApportVersion: 2.20.1-0ubuntu2.5
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC0:  seemas     2524 F.... pulseaudio
   /dev/snd/controlC1:  seemas     2524 F.... pulseaudio
  BuildID: 20170201180315
  Channel: Unavailable
  CurrentDesktop: Unity
  Date: Wed Feb  8 21:26:44 2017
  Extensions: extensions.sqlite corrupt or missing
  ForcedLayersAccel: False
  IfupdownConfig:
   # interfaces(5) file used by ifup(8) and ifdown(8)
   auto lo
   iface lo inet loopback
  IncompatibleExtensions: Unavailable (corrupt or non-existant 
compatibility.ini or extensions.sqlite)
  InstallationDate: Installed on 2016-11-23 (77 days ago)
  InstallationMedia: Ubuntu 16.04.1 LTS "Xenial Xerus" - Release amd64 
(20160719)
  Locales: extensions.sqlite corrupt or missing
  Plugins:
   Google Talk Plugin Video Renderer - /opt/google/talkplugin/libnpo1d.so 
(google-talkplugin)
   Google Talk Plugin - /opt/google/talkplugin/libnpgoogletalk.so 
(google-talkplugin)
   Shockwave Flash - /usr/lib/flashplugin-installer/libflashplayer.so
  PrefSources: prefs.js
  Profiles: Profile0 (Default) - LastVersion=51.0.1/20170201180315 (In use)
  RelatedPackageVersions: google-talkplugin 5.41.3.0-1
  RunningIncompatibleAddons: False
  SourcePackage: firefox
  Themes: extensions.sqlite corrupt or missing
  UpgradeStatus: No upgrade log present (probably fresh install)
  dmi.bios.date: 05/27/2014
  dmi.bios.vendor: LENOVO
  dmi.bios.version: 9ECN26WW(V1.09)
  dmi.board.asset.tag: No Asset Tag
  dmi.board.name: Lenovo Y50-70
  dmi.board.vendor: LENOVO
  dmi.board.version: 00000000Not Defined
  dmi.chassis.asset.tag: No Asset Tag
  dmi.chassis.type: 10
  dmi.chassis.vendor: LENOVO
  dmi.chassis.version: Lenovo Y50-70
  dmi.modalias: 
dmi:bvnLENOVO:bvr9ECN26WW(V1.09):bd05/27/2014:svnLENOVO:pn20378:pvrLenovoY50-70:rvnLENOVO:rnLenovoY50-70:rvr00000000NotDefined:cvnLENOVO:ct10:cvrLenovoY50-70:
  dmi.product.name: 20378
  dmi.product.version: Lenovo Y50-70
  dmi.sys.vendor: LENOVO

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