Apparently the disappearance of files and directories occurred in all ext4 filesystems, including files and directories usually "read-only" in /var and /usr, like binaries installed for gcc, and several others utilities, like apt-get, aptitude, which we tried to use to do some tests and fixes, but a lot of commands and utilities didn't work anymore, all them were crashed, some of theirs dependencies or files disappeared.
These filesystems were ext4, and this oddly occurred last Friday the 13h (November 13, 2015), at about 4:10pm (GMT-3 DST, Brazil). Some log files of /var also disappeared. But we could get the syslog what started to show a lot of errors just when the users also noted the system anomaly. But these errors were related just to absent of files none explained the event that could cause the disappearance of data or any of kind of hard-disk problems.
As a workaround, we booted with a rescue image, just to try get a copy of the /home data, although corrupted we could recover data form some files. And sure, some data were recovered, but a lot of files and directories disappeared and others were there but truncated (zero size).
There are some known issue that could explain this ? How to prevent this from happening again in the others severs ?
PS: The "storage" was mounted in a hard RAID 1 (between 2 hard-disks)
EDIT - ENVIRONMENT: The machine is down, so I cannot get a lot of info that were there, but it was running Debian:
uname -a Linux XXXX 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt11-1+deb8u6 (2015-11-09) x86_64 GNU/Linux
- Under some NATs
- Internet access to an external (cloud) SVN server (controlled by firewall).
- Internet access to some packages repositories for manual update (apt-get update/upgrade). No one update or upgrade done for months
- Access via ssh