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Read my .sig. Also my original post.
Why do you tolerate how Linux organizes tracks and sectors? Wouldn't it be better if the filesystem was organized around how you like to designate disc blocks instead? Sounds silly, doesn't it? But that's what's going on here. Calibre provides a level of abstraction above the file -- namely, the ebook -- just like the filesystem provides the file as a level of abstraction over the physical disc. Interfering with how calibre manages the files that make up its ebooks can make a mess of things, just like direct disc writes can make a mess of your filesystem (I've seen it happen; thankfully, it was my boss, not me, who bricked the PDP-11). Those files need to be stored in some way that does not tempt people to confuse files with books, or confuse calibre with a file manager, and tamper with its private files.
If you want to do something to one of your pdfs, export it with whatever name you like, do your voodoo, and import it to replace the old copy. Calibre's library files ought to be a database. Treat them as if they were one.
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