Application shortcut causes reinstall/repair of application....

I'm working with an application (win 7, vb.net) and I'm trying to work around some odd behavior of my application shortcut. Here is a summary of the problem:
My app installs and places a shortcut on the Desktop.
I go into my application's directory and modify any files.
Go back to the Desktop shortcut and click on it.The application appears to perform a reinstall/repair and will replace any files I have modified.
I need to figure out what is causing this and how I can fix my application or shortcut so I can stop this behavior.
If I re-create a new shortcut, from the executable, I do not see that behavior but I don't want to have to create a new shortcut in this case.
Thanks. 

This is a feature in MSI when you enable advertise shortcuts and has nothing to do with .Net so your question is off-topic here.
The default install directory is program files which is read only by default. You may want to redesign your app right now if you do any writing in the
install directory. The place to put your writable data is under application data.
Visual C++ MVP

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