[unboggling]

For the Title "Krondor- The Assassins", this is in my only Series column:

Riftwar 05; Riftwar Legacy $ [2]

That construction is:
(broadest-series-name)(space)(most-specific-subseries#);(space)
(most-specific-subseries-name)(space)(varied-author-series-symbol)(space)
([series_index])

I use semicolon rather than period to indicate hierarchy because semicolon looks better and I don't need to see hierarchic breakdown in Tag Browser. The "$" indicates varied-author-series, a clue to sort by title within series rather than sort by title within series within author.

Edit: But that doesn't address the OP's question about automatically renumbering a chosen level of multi-level hierarchical series. Calibre can handle automatic renumbering of only one level per each series-like column, the level that the index applies to, one series-like column at a time.