If it's one large file or a few large files, "du -kSx | sort -rn | less" will catch it.
If it is an accumulation of small files, you may have better luck if you drop the 'S' and try "du -kx | sort -rn | less"
Opinion:
I think 'du' and 'ls' see almost everything. The exception, files in directories that have had filesystems mounted over them.
E.g. You put a file 'bigfile' in directory /example, then you 'mount /dev/sdd4 /example'. 'ls' can no longer see 'bigfile'; and 'du' can no longer see it either. 'df' will accurately reflect the space occupied by 'bigfile'. When you 'umount /dev/sdd4', 'bigfile' will again be accessible. I just mention this in passing. This would not be your problem.
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