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My windows 7 Program Files and Program (x86) files were merged. My computer is still working but not properly. I've tried System restore from and earlier time but it has not improved.

Is there anyway to reverse the merged files to the previous location?

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In order to reverse what happen we would need to know how you managed to do this. This shouldn't be possible both are protected folders, so the only way this could happen, is if you forced it to happen ( i.e. junction points). Its also not clear if both directories still exist or just one. –  Ramhound Jan 28 '13 at 15:19
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I've never heard of that before, did you manually merge them? Well, you can pop in your install disc, and copy over the default windows apps back to the respective folders (I assume that third party apps wouldn't care much, but Windows app's paths are hardcoded in the registry.)

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