MacOS Catalina issue: Application Icons missing from Icon Chooser

Running MacOS 10.15, KM 9.0.2

A fare number of icons in my palettes have gone generic after Catalina update as here near the bottom:

.

Going back to the icon chooser they're missing as well:

.

Some make sense as they're depreciated apps in 10.15 like MS Office 2011 and some Adobe apps still need to be updated. Other like Apple Mail, Apple Notes, Apple Messages, and Apple Contacts do not.

Neither restarting or rebooting helps.

Suggestions? Preferences to delete maybe?

The ones with a "denied" symbol over them are as expected, the system puts that over the application icon if they are not compatible with the OS.

Catalina moves the system applications. Although they all appear to be in the one combined "Applications" folder, the system applications are actually no longer in /Applications, they are in /System/Applications. Keyboard Maestro 9 searches /System/Applications as well for icons, so it should find them.

I see in your Icon Choose, it is showing Notes.

You can run the commands:

/usr/bin/mdfind -onlyin '/Applications' 'kMDItemContentTypeTree == "com.apple.application"c'
/usr/bin/mdfind -onlyin '/System/Applications' 'kMDItemContentTypeTree == "com.apple.application"c'

to get a list of the Applications that Keyboard Maestro will look at (Keyboard Maestro also looks in ~/Applications and /Developer/Applications).

Then for each of those it will ask the system for the icon for that file.

So it may be Spotlight not finding the applications, or it may be the Launch Services system is messing up the icons.

Or it could be something else entirely.

They WERE in the icon chooser’s listing and once reselected, show in the palettes. A combo of software glitchiness during the update and not doing complete work on my part.

Thank you for your time and attention.