@davidfor: Because I'm an idiot, I hadn't saved the mangled metadata.calibre file, so I had to resort to some creative manual mangling to replicate my original data set, and, yeah, it seems to behave now, thanks
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Random jq query I used to double-check the metadata sanity:
Code:
jq '[.[] | { Series: .series, Index: .series_index }] | group_by(.Series)[] | sort_by(.Index) | unique' < /run/media/niluje/KOBOeReader/metadata.calibre