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Some publishers are extremely fond of beginning the filename of every file in an epub with the ISBN… and, about half the time, it's not the epub's ISBN, but a paper edition of the book. It's just as annoying as the interminable series of _split000x that results from converting a mobi.
As Kovid says, bulk renaming makes this much easier — and then one can spot the "also by" page in a fifteen-year-old book, and the "here's the first (oops, unedited and unproofread) chapter in the next book in the series," and other ad material, then do with it what is appropriate. Reduces the overall file size and speeds loading on old hardware, too! If you don't like having multiple file extensions for the same kinds of files (for example, both .jpeg and .jpg, or .html and .xhtml), there's also a tool for that in the editor. The bulk-renaming tool leaves the extensions alone.
If one has a scheme for standard naming, that makes later creating an omnibus edition (single epub containing several previously-published, related books — a single-volume The Lord of the Rings, for example) a lot easier, and a lot easier to debug when there are any problems, especially with subtly-different stylesheet entries that have the same name.
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