It will delete (or rather not load) images/fonts/etc if you load an ePUB that has not referenced them correctly in the opf. If you miss that and then save, the files seems deleted.
I noticed that in 0.8.6 for sure. Some books I had under my nose had some images with the wrong extension in the opf, but correctly in the HTML files. They images were not loaded, because I assume the loading process looks at the files in the opf. The book worked fine on readers. It was probably done to punish editing the book (removing watermarks or something).
Anyway, I consider this a different case.
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