This is the default behavior when using .msi package. If any resource is missing, Windows Installer will fix it by running the installation package and installing again all resources from the .msi file. Have a look on Windows Installer Advertised Shortcuts
However, as a workaround, you can try to use .EXE package and check the "Do not delete extracted MSI and CAB files"
option from the "Builds
" page. This way the Advertised Shortcuts will use the package under the "AppDataFolder" folder even if you delete the .exe installer. But if somehow this package also gets deleted, there is no way to run the repair since it needs to run the installation package again.
Hope this helps!