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This can be tricky. The KTE default is to replace the book file in place and 'trick' the kobo into thinking it's the same book. The benefit is that you can replace the book and retain all your bookmarks, annotation and reading position.
This works fine for most small changes, (like tweaking the css of the book, and presumably, any of the settings in KTE itself.. But it will break things in interesting ways if the contents of the (x)html files have been changed/edited significantly, (ie, paragraphs added or removed, files split at different points, files added or removed to the book, any changes to the table of contents, etc.) . It won't corrupt your whole database, but that one book will probably have to be deleted and replaced.
If you are making the kinds of changes to books that will confuse the kobo, you have to either remove the book from the kobo first, or Uncheck the option "Do not treat replacements as new books" in the KTE options. (it's in the "Collections, covers & Uploads" tab. Since I frequently make large edits to my books, including fixing page split issues, I leave that option unchecked.
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