Oh that’s a bit of a surprise as it was a common workaround.
Do you know you can do a Safe Mode start which doesn’t wipe all your data it just does not install all the custom apps.
However if you disable the app and then do factory reset the app will be activated again.
Have you tried removing the Digital Wellbeing app?
Thanks for the hint! I’m going to try Safe Mode start the next couple of days.
Don’t forget to disable the Digital Wellbeing app too 
Sadly today’s reboot lost my Drive, WhatsApp and internet shortcuts again.
I updated to 8901.4.A.0019.1 release-keys the other day. Digital Wellbeing is still disabled.
Disappointing.
Appanently there are other apps other than Digital Wellbeing, that can interfere with a reboot.
Issues on rebooting can come from Google Play Store and Services, as well as Qualcomm Location
Have a look at this topic
I don’t have Qualcomm Location listed in my apps. And Google Play Services can’t be disabled - I 'resume I need it to keep apps up to date.
I guess there might be a way to disable it temporarily in safe mode, but that won’t help me because I only lose the shortcuts once every 10 or 15 reboots. So I might disable it, keep my shortcuts, conclude that Google Play Services was the culprit, and be 100% wrong.
Looks like I’m back to relying on bookmarks in my browser to not lose internet shortcuts, and using favourites in Drive to find my frequently opened files, and just searching WhatsApp for groups.
I’m not suggesting you disbale play services as it will cause loads of notification about what won’t work, like the camera even though the camera is fine, with it disabled.
I havbe Google Play Store, romoved, which stops the Play Services from updating unless maybe I get it from the OS update.
But it can be disabled and there is an option to uninstall the latest Google Play Services.
You may like to look into that a bit more ??
But then how would I install new apps from Google Play Store and keep the existing ones up to date (which is usually a good idea from a security perspective)?
Are you suggesting to disable it most of the time and just enable it once every X weeks to upgrade/install apps?
Sadly , I’m not suggesting it as I don’t use the Google Play Store, but you could try for a while, bit then if this only happened this once, with an OS update it’s probably not worth changing anything to see if it works, that’s probably more work that recreating the shortcuts
Well this is a turn up for the books.
I’ve just restarted the phone via the screen gui and lost my Firefox short cuts and my four contacts shortcuts.
It’s never happened in the two years or more I’ve had the phone and no OS updates etc.
Will try out a few ideas ??
UPDATE:
By powering off and on using the power button they came back.
I rarely re boot the phone
“via their screen gui” - didn’t even know this was possible! How? I always use the power button.
If the home screen is not locked hold the power button for two seconds and a screen menu appears.
Middle option
Ah ok, I thought that’s what you meant when you said “by using the power button”.
See my post 49 when I also encountered the problem through a restart (though from the bootloader not the OS) instead of my usual off/on. Maybe a developer could try to see what difference that makes.
Final update. Phone was stolen last month so this is a moot point for me now. I’m on to FP4.
So we FP3 owners are on our own now… 
The problem seems worsened after the latest update (8901.4.A.0021.0). Some observations:
I have disabled the digital wellbeing app, btw.
I’m wondering what you mean, ??? You think there will be no more updates to the OS ?? I’m sure there will be ?
Fairphone have just issued an update, albeit the final, for the FP2
FreekB just meant that, since el_foz had their FP3 stolen and is replacing it with an FP4, there’s one less person in the debate.
Of course there will be updates for the FP3.
Wow! my brain must be loosing cognitive powers quicker than I thought, as whereas I understand I didn’t and still have problems reading it like that.
Better get to bed before I loose my way completely. 
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