That was what I was expecting to see. If you want to save a few keystrokes you can just use yay but everyone has their own way of maintaining a system.
Which is better, pacman -Syu, or yay -Syu?
Neither?
pacman -Syu updates your repo packages.
By default, yay -Syu updates your repo packages using the equivalent of pacman -Syu and then updates all your AUR packages.
I think the point he was trying to make was that yay -Syu and yay are exactly the same except the latter is faster to type.
Either way, I don’t think any of this has anything to do with your issue. Based on your pacman.log info, I would say your missing cookies are not likely to be related to that update.
If you reboot again, do your cookies get removed again?
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No, it doesn’t. Rebooted to check.
On my machine after an update Dolphin and Gwenview’s window size got reset today . They remember the size and position usually . So maybe sweeper configs got reset and purged your passwords and cookies 
. Check if site settings are also gone
I forgot to say that Dolphin stopped showing thumbnail previews too. Configure Dolphin > Previews and clicking Defaults helped to get back the thumbnail previews. I read it somewhere in the internet.