Invisible Files in Windows 7, 8 and 10 Program Files

Summary

First of all – it is not a virus! It is not a bug either. It is a feature, that doesn’t allow legacy applications to write files inside Program Files directory.  This feature allows legacy applications think that they are writing to a system folders.

Symptoms

You can see your custom files inside one of the Program Files directory folder through your application.  You can open them and view them and modify them..  However, if you open the same directory in Windows Explorer, your files are not there.  You can’t see them, even if your a super administrator of all administrators.  What is the Mystery?

You can see your custom file inside a folder somewhere in Program Files directory But you can’t see your file through Windows Explorer in the same directory

Explanation

First: You do not see the files because they are not there!

Instead, they are stored in VirtualStore directory in %UserProfile%\AppData\Local

If you navigate to this location, you can see that all three system directories (Windows, Program Files (x86) and Program Files) have a placeholder here for older application to work and not to complain.

Any time your legacy application needs to write an INI file, or store some configuration information in system folders the corresponding file will end up in %UserProfile%\AppData\Local\VirtualStore directory.

Windows Explorer offers a special button – Compatibility Files – so you can quickly jump to a corresponding VirtualStore directory.

To return back to your corresponding Program Files directory, use Backspace.

Reference:

Invisible files and / or folders in Windows 7
http://social.answers.microsoft.com/Forums/en-US/w7files/thread/d73dd67c-f7d4-4d2d-886e-b774141bd24f

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