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I've been repairing a Windows 7 64-bit installation. In the process, the Windows partition was subjected to several rounds of automatic repair, chkdsk, sfc, even a volume shrink. Long story. Anyway, after I'm done, Windows mostly works, but it seems that all NTFS junction points - like c:\Users\Username\Start menu - are not junctions anymore, they're just empty folders.

I can't really tell on which stage did this happen. Stages were many, and Windows won't boot in the meantime. The filesystem on the partition was NTFS all along though.

Is this a known condition, is there a wholesale solution to this? Barring that, is there a user profile fixing routine which restores the proper folder/junction/permission structure?

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If that is true, then you WinSxS directory is probably screwed up. Some program may fail to run. –  vcsjones Apr 30 '12 at 12:58
    
I've scanned Windows\WinSxS on another Win7 box - didn't find any junctions. So probably not. –  Seva Alekseyev Apr 30 '12 at 13:23
    
Cave and pave, or use a restore point. –  Moab Apr 30 '12 at 14:18
    
@vcsjones: I though WinSxS uses hardlinks, not reparse points? –  grawity Apr 30 '12 at 15:49
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Hardlinks should not be affected. To kill a junction, it's enough to flip an attribute; hardlinks are just regular file records. –  Seva Alekseyev Apr 30 '12 at 16:33
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