Well in my experience there is no such thing as 100% with computers. There are just too many tens of millions of instructions going on at so many levels, hardware and software, and many of these levels have been abandoned for decades in the deepest parts of the OS. Hardware, being subject to physics, suffers the results of entropy and that can in turn degrade the software if there is a feedback loop. I’m not saying anything new here, just that I don’t think anyone can say even Notepad.exe is 100%. 
So that aside we have statistics, and you’re definitely going to hear more problems than not, and especially so on a technical support forum that spans back into the beta eras of this software. The huge majority have been using Scrivener, as you have yWriter, for years without hassle, and most of them never even come to the forum. As for my own anecdotal experience, I’ve of course been using Scrivener for Windows (and often in a capacity which pushes its limits further than routine use would demand of it) ever since before it was released as an early public beta—and I’ve yet to lose a single word in it. The Mac version, which can’t really be compared even though it has similar protective measures, I’ve been using for close to seven years now for real and “testing” purposes—and again, I’ve never lost a single letter.
Yup, it messes up sometimes (though more often it’s the system underneath Scrivener that messes up; especially so when complicated by third-party software that synchronises work automatically to servers) so the best we can do is build protection into the system to defend against that as best as possible. As with yWriter, we make routine backups of your project. Whenever it is closed, a zipped copy of the entire project is created and stored away in a safe place away from where it cannot be accidentally deleted. By default five copies are saved in this fashion before rotating the oldest one out. This can all be changed in your program options. You can for example have the backup folder arrange to put files on Dropbox, which will in turn protect you from a total system crash, especially if you use more than one computer with the account. You can also set it to backup when you open as well as close, or even whenever you hit Ctrl-S. It can be instructed to never delete old backups as well. In addition to all of that, you can (and we encourage you to) make routine backups of your own that are outside of the automated system. This is very easy to do with the File/Back Up menu.
Meanwhile, the format is auto-save oriented. Every time you pause for more than a couple of seconds, your work is written to the disk so that in the even of a crash you shouldn’t lose more than a few minutes if not seconds of work. Inside the project itself, you have Snapshots (think versions), which protect all of the individual pieces. You take a snapshot and it becomes an immutable frame in time for that piece of the book or background file.
Is that 100%? Of course not, but is it safe? I would say so. Data loss errors resulting from the software itself are from what I’ve seen, far less common than OS crashes, hardware failures, and other such issues.
I hope you like the software, I know it really suits the way I like to write and structure documents.