There are multiple suggestions that piecemeal this idea already, but the premise here is to store every story element from characters, to places, to items, to McGuffins, etc. in a series bible that can be accessed from within any book in the series, allowing the user to "insert" that element via check mark into the active book.
Alternatively (or additionally), each element can be inserted into a selected book directly from the series bible by checking off which books that element may belong to (example: Bob appears in Books 1 and 2, but not 3, so the user would check the boxes for 1 and 2 beside his name, and he magically appears in Book 1 and 2's character list, but not in 3's).
For a more granular approach, the series bible could also have a list of changes from book to book, where a character would display a particular trait or attribute in book one and a change in that trait in book two (this could be noted inside a list of custom attributes that also have checks representing book numbers--Bob, for example, has the attributes "jerk" and "nice guy" defining him, but the attribute for "jerk" is checked for Book 1 only while "nice guy" is checked for Book 2, indicating his internal change from one to the other), or a "pristine" location in book one will be "damaged" in book two, even though the location description would have attribute tags denoting each state (just with different check marks) etc.
I think this check mark method would be a quick and easy, on-the-fly way to keep track of every series element, its position in each book, and how it's used in each book, not to mention less of a headache for the author of a series that spans more than three books to monitor his or her progress, verifying when and where certain characters, places, etc. appear in the series (perhaps also allowing a selection for chapters and scenes via check marks in a submenu here so that the writers doesn't have to skim an entire novel to find each reference), and ultimately staying about as well-organized as one possibly can when writing a series.