The Case of the Many Blanks

[Saturday, May 24 at 04:50 AM UTC] Erratum in The Case of the Many Blanks: The last line of the first section was changed.

# _ _   _ _   _ 1 _
# _ _   _ _ _ _ _ 5
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# 4 _   _ _   _ _ _ _
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_ _ _   # _ _   _ _ 12 _ _ _
# _ _   _ _ _ 10 _ _
_ _ _   # _ _   _ _ _ _ _ _ _ 8 _ _
_ _ _   # _ _   _ _ _ 6 _ _ _ _
# # _ _   _ _ _ _ _ 11 _ _ _ _ _
# # _ _   _ _ _ 7
# # _ _   _ _   _ _ _ 9 _
… 12 more …

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"_"  _ _   _ _ _   _ _ _ _ _ 2
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_ _ _   _ _ 1 _ _ _ _ _   _ _ _ _ 4 _   _ _ _ _ _ _   _ _ _   _ _ _
_ _ _   _ _ _ _   _ _ _ _ _ _ 8 _   _ _   _ _ _ _
… 19 more …

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… 20 more …

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_ _ _   _ _ _   _ _ _   _ _ _ _   _ _ 6 _ _ _ _ _ _ _ _
_ _ _   _ _ _   _ _ _   _ _ _ _ _ _ _   _ 5 _ _
… 21 more …

_ _ _ _ _ _ _ _ _   3 _ _ _ _ _ _
_ _ _ 1 _ _ _ _   _ _ _ _ _ _
5 _ _ _ _ _ _   _ _ _ _ 8 _
7 _ _ _ _   _ _ 2 _ _ _ _
_ _ _ _ 4 _ _ _   _ _ 6 _ _ _ _ _

 

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Hints

How do we start this puzzle? You are looking to populate the blanks with installations in several book series. Using the unique punctuation and the number of books in the series should help. Also, series with certain repeating structure to the blanks (found in all but the 3rd section) indicate that all books in the series follow a specific naming convention.
There is also a theme connecting all the book series.
We have filled in the first 5 sets, how do we continue from here? The last blanks are similar to the top blanks, they are filled using the titles of five books from another mystery series (not the ones you have already used), each corresponding to one of the five subpuzzle answers. The title of this puzzle directly references this series.