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This is normal. After safe mode, downloaded widgets needs to be added again while preinstalled widgets are still on the home screen.
@uliwooly
The widgets are all in the internal storage.
@Rickard
I see. It's currently working again (I rebooted few times and no error with loading the widgets. Previously some of the system widgets (stamina mode, clock, music) didn't load properly.
On another note, I realise that after my safe mode reboot (I'm now back in normal mode, my saved accounts only has Google (I need to readd others Eg Dropbox). Is this behaviour also normal?
Yes, also accounts created by downloaded apps are missing as well. The app itself keeps its data though.
I'm not sure why this happens but it might be that in safe mode, it's like the app has been removed so system apps, like our launcher, will think that the app has been uninstalled.