[Adoby]

While it may be difficult to tell you what would be "good practice" for you, it is possible to give you an example of what is bad practice.

Don't access the books from inside the calibre library. That is dangerous and confusing, since the library is not meant to be used directly. It is possible, but not recommended.

The reasons are that the library structure is hardwired into the calibre software, and the library contains information that is only meant to be used by the calibre software. For instance the paths and the filenames are most likely unsuitable for direct use. There are numeric id inside parentheses. There are cover files and backup data for recovery (.opf). The filenames may be abbreviated in a weird way. And even very minor manual changes to any file, path or filename may result in data loss, if you are unlucky. Stay out! If you ignore this, make sure you have a recent backup of the calibre library, and be prepared to restore that backup.

Also the book files inside the calibre library may not be updated with the latest metadata. One reason is that some book formats don't allow all metadata to be stored inside them, another is that updates of metadata in calibre are optimized by the use of "lazy updates". That means that minor changes of metadata are usually NOT stored in the books inside the calibre library. They are only stored in a central database file, metadata.db. The reason is that it would be very expensive/slow to update the metadata inside the books all the time, even if the format allowed the metadata to be stored. They book files would have to be copied, unzipped/exploded, updated, zipped/packed, copied again and finally replaced. And all this for every minor change.

I've seen people complain about calibre taking long to resort the books after a bulk update of metadata, and the latest version has been given the option not to resort, in order to speed up bulk metadata updates. I can only imagine the level of frustration if lazy updates were not used...

When you save books to disk, send to device or convert to another format (or the same) the new books will have the updated metadata. Also the GUI show you what the updated metadata is.

It is possible to force calibre to update the metadata in the books. That is where polish, epub update and conversion to same format is used. But as long as you just access the books from the GUI, save to disk or send to device, you get books with the correct metadata. (When you open a book in a reader, from the GUI, the metadata that reader has access to may not be the updated metadata.)