The utility you call [the WHS cleanup utility] is not a Microsoft product; if you mean "Windows Home Server Cleanup Tool 1.0 ".
From what I read, via internet search, it is not very controllable. no check and balances, and will delete any and all refrences to the file[s] it deems 'unreadable'.
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You must check the contents of the .cmd file prior to running it! I have found it to be correct, but you don't want to be surprised, upset or experience any unpleasant emotion after running it. If you don't feel OK about running it, then
don't.Running the .cmd will delete the reparse points, effectively deleting undeletable, unreadable files.
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If, a big one, you read and tried the other tests to remove file confilcts, and had no success; I might suggest a brute force hardware approach; since you indicated your WHS went up in flames .. via the Hindenburg refrence...
One: Buy one or more external drive enclosures / usb to IDE[anything]/sata adapters.
Two: Shut down the server, as 'gracefully as possible, and physically remove the drive[s] [[ labeling each one, to return to the server later]] and attach it / them to the USB adapter.
Three: On the PC / client OS of choice that can read and write to NTFS volumes, plug in the USB adapter, and wait for the unit to be detected.
Four: Run appropriate disk/voluime/file checking utils to salvage what you can.
Five: Open Explorer or equivelant to see folders and files.
Six: Navigate to path similar to [USB adapter drive letter]:\DE\shares. This is where your files should be located.
Seven: Select and copy folders and files to another local drive.
Eight: Software dismount and power down, and remove the USB adapter / drive.
Nine: Repeat steps Two thru Eight until you have all of your files.
Ten: Reassemble the WHS Media Smart Server, and reboot, If you did all as stated above, with no deviations, The SERVER should boot back up and be in a condition, no worse than when you started, my suggestion.
HTH
PVM