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Calibre and chapter breaks: Solved
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I've used a MS word document or PDF if there are vector separators in the text without any issues by uploading it directly to Amazon. If I need a mobi for BookFunnel, I just go to Draft2Digital and get one in minutes. In fact, I have changed from uploading to Amazon to going through D2D as my distributor which makes it much easier. The book is formatted and I don't have to play with Amazon and their dashboard, keeping it like more like a publishing house would,

Question B.A,
Do you mean uploading a pdf or MS Word for Kindle, too? If you did that would you not have issues (without Html) with other platforms like cellphones and such?

Over the past couple of years, I've learned to just keep things basic and it works better.
The problem is that Calibre seems not to handle the page-breaks we put into the text at chapter ends. And that’s an annoyance. But today, I finally figured out why it wasn’t working: It’s an oddball combination of a MS Word defect, Calebre’s not taking that into account, and the natural inclination of authors to place the page-break after dropping in a few blank lines below the last text before calling for the page-break.
Calibre does handle chapter endings perfectly. But, only if it recognizes them. And if we give it the file that Word produces, it won’t, because Calibre's criteria is clear: Text is followed immediately by a manual page-advance. A blank line between the last active line and the break and that break request is ignored.
The problem is, Word defaults to a blank line before inserting the break. If you place the curser after the final period and type a manual page advance (Control-key + Return-key for the PC and Command-key + Return-key for a mac) and you get a paragraph mark dropped in before the page advance command. So, Calibre then ignores the page-advance and we assume the problem is at their end.
There is a trick to fix it, though.
1. Make the formatting characters visible. (Control-key + 8 for the PC, Command-key + 8 for the Mac). At the end of each line you’ll now see a proofreader’s symbol for a paragraph change: ¶
2. At the end of the chapter find the Page-Break. Place the cursor between the last printable digit of the line and use the delete forward key to remove all the paragraph marks. Repeat for each chapter, then use the procedure that made the formatting characters visible to turn them off again.
3. That’s it. Use Calibre to convert the file and look at the result. It will definitely make you smile.
Hope this helps.