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Shortcut target path is reset during minor upgrade

I have basic msi installer, working fine. Except minor upgrade, when I install the app into different folder then default. 

  1. Install app into changed folder.
  2. Works fine
  3. Increase version number and changed package code 
  4. Perform the minor upgrade
  5. Everything looks good except the desktop shortcut, it does not work, because its target path is set to default installation path, not to actual. Working directory is correctly set to actual.

Any Ideas why this can happen?

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