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Hi Robin,
Most of the times the difference between du and df are due to temporary files that has been deleted but that they are still in use by a process till the process end and release them.
Options:
1) If you remember what file you removed maybe you can track the process it used it (typically with log files).
2) Check with lsof to see what processes has anything opened on that directories.
3) Restart the box...
Best regards
jose
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