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I forgot about this problem, and sync'ed my kindle when I bought an ebook today. I've used calibre to convert epubs to mobi, but then copy the files manually to the kindle documents folder. I shy away from most apps that "sync", 'cause usually I don't get the expected results.
Since I leave wireless off most of the time to extend battery life, this issue doesn't pop up too often. But if I use the "send to kindle" on the Amazon side, turn on wireless and sync, then any of the manually (side-loaded) books on the device get deleted.
I guess Amazon doesn't consider your kindle storage to be sacred or personal. No respect for boundaries.
Fortunately, I only had two books I was reading that got whacked, and replacing them was easy from my PC copies. Now the challenge will be to remember to copy the file from a new ebook down to my PC (which I think is an option), and then copy it to the kindle. Next time.
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