ThinApp patches and upgrades work by not replacing the original .exe but by adding a new main container. When the original is run, it searches for any newer containers and uses the newest one instead, completely disregarding its own contents.
For example, given the following ThinApp packages:
If present, when winrar.exe is run this will be run instead.
This would be chosen over winrar.exe and winrar.001, and so on.
Since the original ThinApp package will always run the latest upgrade (unless the upgrade packages are removed from that directory), the signature scan will only detect the latest version of the ThinApp package.
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