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Regarding the problem of collections empty or almost empty when jiembe updates the metadata, it's something that also happens to me when I choose to manually update the metadata on one book. Afterwards, most books loose their collections association. It isn't something that I do frecuently, and knowing the problem I usually avoid doing that. I think there's something in the plugin configuration causing this, because I read other people is doing this without problems. I think maybe it's because I have it configured to only send metadata when I send the book, but not to automatically update the metadata of the books already in the device. I should try to reproduce the problem in my Kobo Mini now that it's retired, but I don't have the time.
Anyway, jiembe, just in case you haven't realized how the series information works in Kobo. When you send the book to the device the series don't appear, Calibre needs that Kobo firmware process the book and adds it to the Kobo database, that happens when you copy the book in Kobo and afterwards disconnect Kobo from your PC. The second time you connect the Kobo to Calibre, Calibre automatically sends the series information, you don't need to do anything or force the update of the metadata of the book.
You only need to manually update that metadata if you change it in Calibre after the book has been processed, and there's some configuration in the plugin to do it automatically if you want to (I think, I don't have it configured myself)
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