Instead of prepending series to title manually in the column Title in the calibre library, you can use Metadata Plugboards (Preferences - Import/Export) to do that automatically whenever you Send a book to Kindle or other device. These are my Metadata Plugboard settings for Kindle:
To prepend Series and Series Index to Title in destination field title:
Code:
{series}{series_index:0>2s| | - }{title}
To sort author correctly; in destination field authors:
If you really want the metadata updated in the ePub format that remains in the library, you can use the third-party plugin Modify ePub to update the metadata in the ePub format of a selected book without doing a conversion. In the plugin uncheck everything except the last option, Update Metadata.