How does it not save the series and series index? Or maybe where is it missing from?
If you do a save-to-disk, calibre should update the metadata in the book to contain the current metadata the library has. But, that means the format must be one that can include series info. Epub can but MOBI does not. You can use a metadata plugboard to put the series info in the metadata for those formats. The common place with be a prefix to the title.
Or did you want the series info in the file name? In that case, you need use the save-to-disk template in the preferences to set the file name.
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