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Grant, for what it's worth, I have the same problem as I use a Kobo and side-load 99% of my books. As I have over 3100 ebooks loaded in Calibre, it's a pain to have to update series metadata manually as you potentially have to select your entire library (slow because the database is on another machine).
What I have done is have a view defined using the View Manager plug-in purely to send to device; I ensure I have the date modified column visible, and sorted in descending order (i.e. most recently modified first). Then when I've sent to the Forma, ejected, allowed it to process the content, and reconnected it, switch to the Send to Device view, then I just select the books I have recently modified and then do the device action. Otherwise, it takes forever to select the complete library. (Then I have to remember to switch back to my default view...)
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