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Windows Server 2008 backups

can anyone describe how server backup works? Here is why. I show a directory C:\public\departmentA\work_in_Progress\customerZ\ArchiveFiles\project23.xls erroring out as not there, the famous "Error [0x80070003] The system cannot find the path specified" error. I went back and looked at the three backups prior to this one and the directory and files are not there. And the path and directories are not found currently. So how does Windows see this path and file if it isn't there? i think it is possible it was there at one time perhaps but it isn't now and wasn't before. Is that directory and contents stored somewhere? I just dont understand how this works.
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The backup process works as follows:
Step one - initialize MS VSS Service
Step two - create snapshot of the data bitmap
Step three - create the virtual container for backup
Step four - Start writing the data from drive to storage according to the information received from data bitmap.

Now to the problem itself. I am not sure 100% but it seems so that information about this data location is written in MFT and to some reason it was not deleted or corrected after you moved the file.
Try to run CHKDSK x:/f (where X: is a partition drive letter) on all volumes this usually removes empty records and crosslinks.
Then try backup again.
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Thomas Rush
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Wait, is it a file backup or a drive backup?