Hi Matt,
This issue occurs every time the apps are updated. For example, Discord is installed in the following location:
C:\Users\AppData\Local\Discord\app.[old_version_num]\Discord.exe
When Discord updates, a new folder with the updated version is created.
C:\Users\AppData\Local\Discord\app.[new_version_num]\Discord.exe
However, the registry still points to the old version.
HKEY_CURRENT_USER\Control Panel\NotifyIconSettings#####\ExecutablePath
There is no resolution for this issue. But you can run a PowerShell script to show all Discord icons. Please see the PowerShell script posted by "g0ph3r532" in this Reddit thread.
You can run that script from the Startup folder if necessary.
Standard Disclaimer: There is a link to a non-Microsoft website. The page appears to provide accurate, safe information.