Thanks for the more comprehensive fix Brecht.

The real problem here is that the view layer should not be NULL, if that's the case lots of other things can break too.

@Campbell Barton (campbellbarton) Looks like one of the toolsystem <-> workspace things you were working on last week.

Here is my suggested tactical fix

Sorry to hear about the add-on issues, but those can arise when saving user preferences, if the add-on for instance crashed before.
The add-on in question is quite complex and is in Contrib folder for a reason of not yet being stable enough.
Generally Blender has the startup blend as the primary way of storing settings. So any add-ons and settings will be stored there if the startup file is generated while they are enabled. That means that both files can have add-ons enabled, which can lead to issues of the errors being present. userpref.blend will override certain settings like theme, add-ons enabled and various other User Preferences settings.

Hate to play straight into your hand, but sadly i have to abide by the tracker rules an close this as a feature request. here's the standard blurb, sorry man!

.blend file requested by @Clément Foucault (fclem) on twitter.

Hello guys, since the thread I lost 5 times linked data with no warning, last time today. The linked node groups simple disappeared from the scene, no warning at all, no orphan data appeared in the Outliner, nothing. As talking about a few hundred materials with 5-6 textures per material + all the material settings it is significant time to remake, especially to do it 5 times.

Am sorry, but this is not manageable issue. We need clear reproducible cases, with needed .blend files, not a monster production case involving lots of different libraries we have absolutely no access to. Further more, you are using original 2.78 release - there were three corrective releases since then (latest official one is 2.78c), and we are about to release 2.79, so… Odds the issue still happens exactly the same in current master code is rather thin anyway. So will archive the report.

Sorry about @Antonio Dipino (Antonio) Vazquez (antoniov), I thought that he experienced all of the things I did

According to @Antonio Vazquez (antoniov) the files did get saved and only the explorer didn't display them. So perhaps you're experiencing a different error?
Could it be that your HDD/SSD/USB device you store on has faulty sectors?

Sunday morning 11:17: I finished re-installing win10 from a backup and downloaded the updates and tried to reproduce the problem again but I was not able to recreate the same error. The screenshots that I gave you in this post was from July 16 2017 at exactly 10:23am (about 3 weeks ago) at that moment I did not have the time to deal with it, so I just came back to windows 7 (I always have a backup of the two OS and Linux).

sorry I forgot to had this: for the microsoft link about "explorer" I never saw it, but i did experiment those problems, but I had those problem with windows 7 and 10 at the same time, including copy/paste on USB thumb drive and external drive. My motherboard was the asus H87-Plus at the time and it had the reputation of having problems with USB, I send it to asus, gave me a new one, the problems where still there, changed my MB to an H97M-E that was recommended to me by my local computer repair store and I stopped having problems within windows 7 and 10 for the USB but the Blender problem persisted on win10. I spend so much time and money that I just gave up and stayed with windows 7 after my original posting (https://developer.blender.org/T50710)

I did it on win10 fresh install, only microsoft drivers, and during that period, since I first thought it was my hardware, I changed my motherboard, my SSD, sent my graphic card to gigabyte for a checkup, tested and stress tested my cpu and memory with legitimate software from intel etc... All of my hardware was double checked and I use only legitimate software, I do not run dropbox, onedrive, torrent or any others, and there is no skype or Steam games running in the background, my PC is for primarily for graphics :)

This sounds like it's probably a general Windows bug - perhaps a strange combination of disk driver, internal caching/background threads, and/or potential interference from some third-party shell addon (e.g. dropbox, cloud sync, TortoiseSVN/Git, AV menu entries, etc.) is leading to a delay in things getting updated?

I am not one of the devs/maintainer, but I'll ask for some more clarification anyway.
When you are talking about the problem of not being able to open and data being "corrupted", is there no .blend-file in the explorer visible (and just .blendX files, where X is a number as shown in the first screenshot)?
Does the .blend-file always appear when you refresh the explorer?
What exactly do you mean by data being "corrupted", does blender show a specific error when you open the project?

Sorry, I should have been more precise. No they don't get saved when they are in this state. If I leave them like that and make my backup, and later come back to work on those files for a reason or another, they just don't open and are considered "corrupted". If I do push "F5" and then backup, if I come back to them later, everything is fine.

That doesn't seem like a bug in blender. If I understand you correctly, the files do get saved, however the explorer doesn't show them?

Here is the image I promised.

'There can be missing image files and missing linked library .blend files, and those are quite different to Blender. Are you saying it's just the image texture that are missing, or are the materials and nodes missing (and so the image textures are also missing along with them)?'

Ok, I'm confused still.

Thanks for the report, but we do not support very limited platforms like raspberry pi at all - those are considered as waaayyyyyy to limited to run a modern Blender.

@J. W. Sargent (NoviceInDisguise) , the parameter allow Blender to run in factory setting. so the issue could be in any add on you enabled / installed or other setting if you run Blender normally. So you could try use a new zip version of Blender, and try enable add-on one by one and see which could be the issue.

Issue has been resolved for now, I am unsure what exactly made this happen, however I am now convinced it is not a bug that can be easily replicated/fixed so a definite solution could be hard to find. For now, try running Blender from the command line with --factory-startup as recommended.

Tested with and without Blender Sensei on latest Blender for Win64 build 2.78.5 (hash 81d7ff8) - Windows 7 64 bit

can't reproduce either, try starting blender with the --factory-startup commandline option and see that resolves the problem.

Win 7 64 bit / GTX 750 / Blender 2.78c

Considering this as fixed for now, then. Thanks for the report.

The issue fixed for me with latest master build. I hope it also fixed for the OP, @Jakeb Ladrey (JLL)

@Joel Godin (FloridaJo), please triage a little bit more careful in the future, just because the user is on windows, doesn't mean it's a windows specific issue.

Windows 7 64 bit.

What OS are you on @Fable Fox (fablefox) ?