This issue can have two possible reasons:
1.) A required file to remove the shortcut overlay icons is missing on your system. Please re-download the most recent version of Tweak-7, Tweak-8, or Tweak-10, and install it. Then try again to remove the overly icons.
2.) The icon cache on your system needs to be cleaned up. To do so, download the attached file, extract the included .bat file and execute it. The .bat file will re-build your icon cache and after a restart of your system removing the overlay icons should work fine.
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