There are a number of bug reports about temp files mysteriously being deleted on Mac OSX el capitan creating issues for Office that uses .docx files (zip files). Just like epub are .zip files. It seems a return of an old issue.... on Mac OS X, there is a dirhelper daemon that looks for files not accessed within 3 days inside the official temp directory and will delete them even if the app using them is still running.
Here is an official apple discussion about this nonsense when it hit under Leopard.
http://lists.apple.com/archives/coco.../msg01595.html
Notice in that issue when it says if you unzip an archive with files that have a modification date of over 3 days old, dirhelper may simply delete them when it runs!!!
This is unheard of behaviour that only impacts software that unzips possibly old files inside the correct temp directory such as Sigil and Office do. For the bug to hit, it must be 3:35am and the dirhelper daemon is run and you have unmodified files unpacked from a zip by the os that uses the zip extended date information to set the original file date.
The file that determines dirhelper's time of launch is:
/System/Library/LaunchDaemons/com.apple.bsd.dirhelper.plist
So please verify your system clock and the time for dirhelper to run from that plist file to rule out any nonsense caused by this strange policy by Apple. Why this bug hits El Capitan again is beyond me?
Related Office bug reports on el capitan can be found here:
https://discussions.apple.com/thread...art=0&tstart=0
and here:
http://answers.microsoft.com/en-us/m...9953eb0?page=3
Not sure the best way to deal with this since lots of Sigil files are unzipped in the correct temp directory to remove issues with attacking temp files creation using races.
It has never hit me, but my clock is correct and I simply do not use Sigil at 3:35am so I have not seen the issue.
Please check that plist and let me know what it says and if your data losses happened near the time set in that plist according to your computers clock, so we can rule this out.