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Duplicate partition makes problems?


I duplicated my NTFS partition.And in that partition some of the folders is not opening " .While opening the message comes "File or directory is corrupted and and unreadable".

Here in my application I use the control code"FSCTL_GET_VOLUME_BITMAP " to get the cluster usage(cluster is used or free) details.And I'm copying only used clusters from my source partition to destination partition.

And I think the files in the duplicated partition not getting the link among them correctly.
Because I am copying the used clusters only so the free space in the source partition is discarded.So I've re-initialize the link...?

Can I do that one...???
How to do that....?
Where I've to make change...? In the volume boot record of that duplicated volume..?

Thanking you

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