[Halk]

No, I'm not trying to save the file over itself. E: is a hard drive array, not the SD card. I've been very careful to ensure that.

However to ensure it's not an issue saving to anything but the C: drive I did the same thing, and aimed at C:\temp. The result was an erased .txt file.

Edit : To be clear, nothing appears on the E:\eBooks directory, or the C:\temp directory. My guess at what appears to be happening is similar to what you're saying. The file is indeed writing over itself, however it's not doing that because I selected the wrong place to put it, it seems to be doing it because regardless of where I tell Calibre to put it, Calibre tries to put it on top of itself.