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About the footnotes:
If you like linked footnotes, then, when you are editing the text, physically move the footnotes to the end of the book, the end of the chapter, or wherever else you want them. Number each note.
Then use "Notes and Links" in the edit menu. Highlight each footnote number in the main text and make it a note. Then go to the footnotes and link each one to the revelant note, by selecting each one as a link.
There are detailed instructions in Harryt's BD tutorial.
You'll find out whether the book cleaner files work, when you load your next book. It's too late for this one.
I'm puzzled that BD isn't saving your work properly. When I load a book into BD I make a Book Designer book almost immediately. (Under "make ebooks", select "Book Designer book". Then, every time you click on "save" it has something to save to.)
There are other ways of achieving the same thing, but this works well for me.
I hope this helps. Good luck with the book.
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