Hi,
Flash Player is saved to C:\Windows\System32\Macromed\Flash on a 32-bit OS. On a 64-bit OS files are also saved to C:\Windows\SysWOW64\Macromed\Flash. The files include the Flash Player version number in the file name, so you would need to account for that in configuring Shadow Defender. The Shadow Defender web page states:
Shadow Defender can run your system in a virtual environment called 'Shadow Mode'. 'Shadow Mode' redirects each system change to a virtual environment with no change to your real environment. If you experience malicious activities and/or unwanted changes, perform a reboot to restore your system back to its original state, as if nothing happened.
With Shadow Defender, you have the flexibility to specify which files and folders are permanently saved to the real environment. This ensures important files and folders are kept after a reboot.
Without knowing anything about this software, aside from what this says, it would appear the issue is with Shadow Defender. If you're being prompted to update after a reboot, it would seem the update is not occurring in the actual system, but in this Shadow Defender virtual environment that restores the system upon reboot. You would need to ensure that the Flash Player install files, whose file names change with each release, are specified to be permanently saved in the real environment.
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Maria