Let us assume a person X has sequenced an application say example Adobe Reader application. He is doing some manual clean up in the package editor. He removed some junk entries to keep the package clean. He also removed the Installer folder that has the installer cache (.msi, .mst, .msp)captured from the installer package as he felt it is also unnecessary junk entries like all others do.
After completing sequencing, he published the package to the machine in a standalone environment and saw that the shortcut icon is missing. He was wondering why the Icon is missing. He came back with a query as why the Icon is missing even after successful sequencing.
Now lets troubleshoot for him. First let's edit the shortcut for icon. We can see that it is looking in %ALLUSERSPROFILE%\Microsoft\AppV\Client\Integration\.....\SC_Reader.ico.
Lets take Procmon capture to get a proper solution. We can see that it is searching for SC_Reader.ico in the Installer location and the path is not found clearly from procmon trace. When checked manually in the %Allusersprofile% we do see that the Installer folder is missing. This is because the person X has removed it from the package considering it as Junk entries earlier.
We can clearly see that after doing a fresh sequencing of the application that the Icon files are indeed kept in the Windows\Installer folder.
So to conclude do not remove files and folders blindly considering it as junk entries. Do not remove Windows\Installer completely. Perform cleanup with caution. Make sure if removing the Installer folder completely will not affect the functionality.