As to the whole "keeping the seat" warm issue.
Janeway is a canon character with 7 TV seasons of episodes and character exploration. It would be very difficult for a non - canon character introduced in the novels to EVER have the story potential that she does. So even though the character of Afsarah Eden was fascinating and interesting and undoubtedly fun to write, an author that loves Voyager as much as Ms. Beyer does would likely give up a lot to get a chance to write a story with Janeway in the starring role.
As much as the fleet exploration concept was interesting, in practice it had to be a bear for the author to keep track of and organize. There are literally dozens of minor characters in that fleet that would have been difficult for any new author to depict properly and would have sent most readers to Memory Beta just so that they can remember who Lieutenant Wehardlyknewyee was. So the easiest way to fix that problem is to cause half the fleet to be lost in a titanic struggle, and now we can go back to the main characters - which is why we bought the book in the first place.