That's weird.
but first you could run sfc /scannow
if there are error that sfc didn't fix you could try Dism /Online /Cleanup-Image /RestoreHealth which is explained here
DISM - Repair Windows 10 Image - Windows 10 Forums
you could also try to run this on powershell
Get-AppxPackage -AllUsers| Foreach {Add-AppxPackage -DisableDevelopmentMode -Register “$($_.InstallLocation)\AppXManifest.xml”}
it will go through every appxmanifest on the list and reinstall it. like if you open the start menu you can see some apps reinstalling like when you do it through the store. so nothing critical about it. (it might give an error with Microsoft.Windows.ShellExperienceHost_cw5n1h2txyewy!App package, that's just because it can't access to it. but it's not a bad error or something to panic about)
it's strange your icons disappeared but maybe these things can help. I have tested sfc and get-appxpackage and it fixed what I messed yesterday when I deleted Edge folder and all. so if it doesn't help, it won't make it worse. still you could do a system restore point if you want before trying them.
You could have gone to restore point when you woke up and saw your system strange with missing icons. but I don't know if you would do it now that some hours have passed.