I was going to post about this as well.
We have played up to book 5 and I found the game extremely easy with 4 players. I did search the rules and book setup sheets but found nothing confirming either way.
There is a rules clarification document in the files section that states HPHB is not a campaign game and to restart with the base deck but provides no point of documentation. I would hope the developer will comment on the topic.
I could see flushing allies and objects at the end of a book but keeping a single copy of each spell... those carry over in the story books.
Thanks for posting the question.
This isn't an open question. The rules for each game state that players start with the basic ten card decks.