Hi Bob,
I have checked your update script and it does not execute any action or function to remove a Shortcut file. So your web update executable does definitely not remove the "Tournament Keeper v8" Shortcut file.
BTW, I noticed that your "Digital Signature" is set to "No". So it's very well possible that an "external" program (e.g. anti-spyware, anti-virus, etc. tool) removes the Shortcut file for you.
Just for fun, you can add some code to your update project to check if the Shortcut is still there after running the web update. Similar to the code from the attached screenshot.
Hope this helps a bit.
Friedrich