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I did a dumb thing and now need to undelete some files. In fact, I have already recovered the files using Glary Undelete, which has served me well on the other rare occasions where this has been necessary. So I have the files.

The problem is that Glary and the other undelete options I've looked at don't preserve the original folder structure. In this case I have about 3,000 small files that I must match to their original locations in a complex nested folder hierarchy. I could see the full folder paths in Glary before the restore, so I know the information is there; it's just not using that information and copying everything to root of my designated destination, rather than relative to the original location.

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I was able to preserve the folder structure with Pandora Recovery.

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No. Files are deleted by removing their reference from the directory index. The file still exists on the disk (until the space it occupies is overwritten) but there is no longer a reference to tell the restore software which directory it was in.

The trash/recycle bin of modern OSes remembers where the file was before it was moved so it can be restored correctly.

Backup utilities like TimeMachine store a mirrored copy of the file system so that they know were each file was.

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Thing is, the undelete software I used first showed me the original path in the user interface before I started the recovery - it had the information there somehow. –  Joel Coehoorn Jan 27 '11 at 6:22
    
I think it may depend on the file system in use. IIRC, FAT based drives "delete" a file by chaining it's name in the directory to have a space as the first character. In this case, the directory info is available but the first character of the name is not. en.wikipedia.org/wiki/File_Allocation_Table#Directory_table –  Chris Nava Jan 27 '11 at 15:11

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