This happened to me when I was using the Web version. I was in a detailed offsite seminar, using a new Windows laptop (on which I had not had a chance to install the Evernote program locally), taking copious notes, and during the afternoon session I kept experiencing the error mentioned. I kept losing pieces of what I had entered. After a while I noticed that multiple versions of the note had been spawned through this process, and I ended up with four different versions. I couldn't take the time to evaluate which note, if any, contained the complete set of info, so I quickly opted to download the application and start up with whatever I could select as "the note," and carry on from there. This worked. I had no trouble when using the installed program, and it seemed to sync ok and save my content in that particular note. I was then able to come back to the office later and painstakingly do a side-by-side comparison among these four notes to make sure I assembled one note that contained all the content. Not sure if there was anything lost in this process, but I think I have everything.
I assume the issue was an intermittent wifi glitch, but man, that's stressful. No one likes seeing their work literally disappear before their eyes! I don't think I'm ever going to use the web app again for anything but a one-shot note. Too much at risk. If the application itself remains stable as it seemed, I'll just make sure I put that on whatever computer I'm using first, and then go about my business from there.
(And by the way, "merge notes", to me, does not mean the same as "append notes." Putting the four notes together one after the other in one note was not what I expected when I chose the option to "Merge notes!")