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I have a Mac laptop and a Win desktop. I wanted to backup data from my Mac to my Win Hard Drive so I connected my hard drive through an external case and connected it via USB to my Mac.

I copied 40GB to one of the two partitions (non OS partition) and 50GB to the other partition (OS partition). Everything went fine and no errors appeared.
When I connected the hard drive back to my desktop I saw no copied folders, but the space was occupied.

I tried a dir in the console, I tried software both on Mac and Win to see used disk space, Daisy Disk in Mac and TreeSize in Win. I see something like 100GB used, but if sum the size of every folder within the partition, I get only 50GB (in the OS partition) and I can't see where are the other 50GB. If I go inside the partition, select all folders and click proprties, the total size is 50GB.

In the non OS partition I removed all the files and formated it, but I can't do that in my OS partition and I'm missing 50GB. I've tried defragmenting and disk correction, seing hidden and system files and folders, deleting Shadow Drives, booting in safe mode with no network, re-connecting to the Mac via USB, etc... and nothing!

Does anyone have any suggestion on how to remove that used space without formatting that partition?

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I can think of three things that might be causing this. One, folders with the hidden or system attribute(s) set are hidden by default in Windows. Two, cluster size; if you have lots of small files, it's perfectly possible for actual disk space usage to be a lot higher than expected. Three, hardlinking that does not get copied properly; Windows uses "hard links" in some places to allow the same file to be accessed under different names. –  Michael Kjörling Dec 13 '13 at 15:46
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What is the filesystem on the Win Hard Drive? If the filesystem is NTFS, do you have any software like Paragon, NTFS-3G, Tuxera, that supports writing onto NTFS? –  MariusMatutiae Dec 13 '13 at 15:46
    
@MichaelKjörling I have all hidden system files and folders being shown and still I can't see the folder. I have big files and small files, and before I copied the folder I had 50GB used, now I have 100GB and the total size of the folders I see the hard drive is 50GB. I have Paragon NTFS in my Mac, otherwise I couldn't work with the hard drive. I've used it before with no problems. –  ricohete Dec 13 '13 at 15:58
    
It is really important to know which file system is on the Windows drive. It could be exFAT but non-Microsoft systems usually have a very poor support for exFAT so the file system could get corrupted during the copy. I would recommend checking the file system integrity on the Windows computer. –  pabouk Dec 13 '13 at 16:37
    
The file system in the Windows Drive is NTFS. How can I perform a system integrity check on Windows? –  ricohete Dec 13 '13 at 16:39

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