I’ve suffered a similar catastrophe a year or so ago. What happened is that I hit Ctrl + S to save a file in a dynamic ClearCase view. It just so happened that at that exact moment, our ClearCase server decided to take a nap or something. At any rate, Notepad++ froze for a good few minutes while waiting for the file access to complete. Then it unfroze, and suddenly the file was completely empty! Even the original content (i.e. prior to my edit) was gone. Now the last part is no biggie, as a simple undo-checkout in ClearCase was enough to restore the original content, but my changes were irretrievably lost.
I’ve had such server hiccups happen when I was editing code in Visual Studio as well, but unlike Notepad++, Visual Studio does not “forget” the content of your file when it happens but merely pops a warning that the file could not be saved.