Thanks - well, I'll try to keep an eye out for it happening. Interestingly enough I have two books missing. The only thing they have in common is that there is a : in the title. Colon isn't supported in hfsplus filenames (not sure about other filesystems).
Calibre is using an underscore instead of a colon when I manually rename books using a colon, but I wonder if there is some specific code path where it forgets to escape it? I'll see if I can retrace my steps.
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