The metadata.calibre is maintained by calibre; dropping books either from the device itself (my books / ... and remove) or from file explorer does not update this file.
Dropping from the Kobo will however update the Kobo database on the device to reflect that the book has gone.
Dropping from file explorer will not directly update the Kobo database; however on next disconnect from the PC that database should be updated
Adding a book to the Kobo by calibre will add the file to metadata calibre, however calibre will not update the Kobo database. The update to the database will occur when the device is disconnected and scans for new content
Likewise adding a file via file explorer will not add the file to metadata.calibre or update the database. The database will be updated when the device is disconnected and it scans for new content.
Also, data such as series info and I believe collections are only synced to Kobo AFTER the books have been added to the Kobo database.
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