disk space disappeared

[Gary Dale <garydale@torfree.net>]

I have a Jessie/64 server that seems to have lost a lot of disk space. 
It boots from a 55G SSD (mounted as /) with a RAID6 array for /home. df 
shows that the SSD is full but I can't find out where the space has 
gone. When I add up all the space in the various directories off /, they 
don't come anywhere near 55G. du -cxh shows only 4.7G being used.

I used tune2fs to set the fsck count for /dev/sda1 to 1 and rebooted. It 
didn't report any errors (system doesn't boot from USB or I would have 
used sysrescuecd).

I also tried using fstrim (although the SSD is mounted with the discard 
option) but that didn't help. The command showed space being freed up, 
but the df command returned the same result.

Any ideas on what is going on?

Below is the output showing the problem.

root@TheLibrarian:/home/garydale# df -ah /
Filesystem      Size  Used Avail Use% Mounted on
/dev/sda1        55G   55G     0 100% /

root@TheLibrarian:/home/garydale# du -csxh /
4.7G    /
4.7G    total

root@TheLibrarian:/home/garydale# du -mxS / | sort -n | tail
34      /usr/lib
34      /var/lib/dpkg/info
40      /usr/lib/gcc/x86_64-linux-gnu/4.9
46      /var/cache/apt
56      /var/spool/cups
88      /var/lib/apt/lists
174     /usr/lib/x86_64-linux-gnu
248     /usr/bin
268     /var/lib/clamav
2329    /var/cache/apt/archives

root@TheLibrarian:/home/garydale# fstrim -v /
/: 644.2 MiB (675483648 bytes) trimmed