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Calibre implements "lazy" update of the books.
Without this feature it can be estimated that at least 24.7 percent of all calibre users would have to be hospitalized due to extreme anxiety combined with panic attacks and high blood pressure, or at least have to take some form of psychotropic medication. As it is now only around 16.3 percent of new calibre users make the same mistake as you did, and think they can "look under the skirts" of calibre and copy directly from the library, without using the save to disk function. However that mistake is only made once, after that this quirk of calibre is learned. It can be estimated that 63.2% of users figure this out from reading the manual or from posts on this forum.
The reason for this quirk, or optimization, is that without lazy updates calibre would become very, very slow. Every little minor change to metadata for a book would mean that the book had to be opened/unzipped/exploded, updated and closed/zipped/packed and finally replaced. If you changed several books, then every book would have to be updated. And to ensure data integrity this update would have to be done separately for every individual change.
As it is now only the entry in the calibre database metadata.db has to be updated. This is very fast. The books inside the calibre library NEVER have to be updated or changed. They don't even have to be accessed. They can stay exactly identical to the original book that once was added, except for the filename. For some users this is important.
Unless you want to update the metadata. If you do a conversion, for instance epub to epub, then the metadata in the book is updated. Also polish and update epub can be used to update the books inside the calibre library.
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