Just to toss this in the mix as a slim maybe
but…
OSX now has this little nifty feature that when you are in a SAVE dialog box and you CLICK on another document name (instead of say a folder and this happens rather frequently) then the default NAME in changes to what you clicked on.
So you are in Scrivener You click SAVE AS While working on SCR1 (Project). YOu then are presented with a SAVE AS DIalog Box and the Default Name is SCR1. YOu navigate to your Projects folder by clicking on Folder Names in the DIalog Box. On Accident you click ONCE on a FILE NAME (not a folder name) during this process. Lets say you accidently clicked on a file named BEER. Tne DEFAULT NAME now in the top of the Save As DIalog Box was SCR1 but is now named BEER. Of course this renaming is done with NO WARNING since it is a “feature” of OSX. You click SAVE. When the warning comes up that you are overwriting (if you are saving in the same directory) you of course click ok because this was your intention.
THe dialog box closes and you go to bed.
The Next Day you go to open the file BEER and you are confounded as to why BEER has info from SCR1 and your dissertation on the lovely uses of Beer has suddenly vanished! ANd your heart is heavy because of course you never made a back-up of the Beer file because you computer is fairly new and a back up is so tedious. 
WHat I am saying is inadvertantly in a SAVE or SAVE AS dialog box it is very very easy to rename the file just by clicking on another file while navigating to your destination directory. This is of course a feature of OSX and independent of 3rd party applications but it is the Number 1 reason OSX users have accidently written over files or misplaced files because of this little documented feature that renames a file on the fly with NO WARNING.
If you want to try it out do this.
Open Text Edit and make a new file. Inside that file type BEER. Save the file as BEER and close it. Put it in a folder on your desktop.
Now open a new document inside that document type the word CHAIR. Now click SAVE.
When the SAVE dialog box comes up navigate to the folder where Beer is saved. You should see one file in there (Grayed Out) named BEER
Click ONCE on the Grayed Out file name Beer and then click Save.
A Warning Box should warn you you are overwriting BEER. Click ok.
Now look you have a text document Named BEER with the word Chair written in it and you never asked to rename it.
This happens more frequently than people realize and is the most common reason for lost files.
The reason is if accidently click on a file name WHILE you are in the process of navigating to another folder you may pick up a file name from another directory level and when you save it in the new directory since nothing is there to replace no warning box ever appears.
Later on as you dig through your files you find two files with the same name and most people delete the OLDER of the two. The OLDER one was the original file (Beer) the new one named Beer is actually the Chair file.
And the OSX never warned you it “did this for you” for convenience.
I am willing to bet something of this nature happened since it is so easy to do…
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