Ebooks: Exporting epub, mobi, iBooks, Kindle using inDesign

Preparing epubs in inDesign:

• You can use older versions of Indesign, even CS4, but each version improves, so it is better to use CC
• Italics and bold will be ignored if they are not applied with a proper character style. Make new styles and Find/replace all
• Same goes for Nested styles: convert these to real Character styles using Find/replace
• Tables: they have to be real Indesign tables, and also anchored within the text, so not in a separate frame
• Unordered bulleted lists: Make those by clicking the list-icon in the Control Window, and not even from a numbered style: that's buggy
• A manually numbered list will render ok, but will lack a space after. You can make a style for the following paragraph, that has extra space before. Or change the style to really numbered by clicking numbered style icon in the Control Window, then it has an auto space after, but the styling will be standard HTML
• Anchor all images within the text (cut and paste into the text), otherwise images will end up at the end of your chapter. Make a new Paragraph style for images, using an auto lineheight
• Also other items need to be within the text-flow. There is only 1 textflow, across all linked frames. If an item is not in the textflow it will be placed at the end of the document, outside the flow. As an alternative you can also use Articles Panel:
• If the order of items is not correct, use Articles panel in Indesign and drag all items in there. This way you can also leave out items you don't want (page numbers etc). Export to epub using this Articles panel > flyout options
• If you don't use the Articles Panel, just choose Export > epub. Add the Publisher in the Export dialogue. After export, you can edit the epub file (which is basically a ZIP containing HTML and CSS) in Sigil (free) or Oxygen (paid). For editing you will need to know your HTML and CSS.
• Use Space Before for every style that need space before, such as headings. Find/Change From the Query list, choose Multiple Return to Single Return. Click Change All. Multiple spaces and returns are not rendered anyway in epub. http://indesignsecrets.com/paragraph-return.php
• Master page items will disappear, so you have to manually override those items. Delete Page numbers, headers and footers: these are unwanted in ereaders, because these are generated by the ereader itself, and will not export anyway
• If a schedule or textual diagram is very complicated, you can convert it to an image 
• If you prefer full colour images instead of greyscale, just update all your images. Full colour images will display as greyscale on greyscale devices. 
• Add the cover as page 1, as big as the page. Use the option “rasterize cover" while exporting. You can also add the inside of the cover. And the back cover at the end...
• Add metadata via File > File info. You only have to fill in title, author, description, keywords, copyrights. The rest is ignored.
• Make a TOC (table of contents) the proper way in Indesign. It is now clickable, at the beginning of the epub, directly on the page.  
• References to page numbers (see page #) are useless, so you have to manually change them. 
• To add chapters that begin on a new page: Use "Split epub" within styles, in the flyout of Styles > Edit All Export styles, or double-click a style > Export Tagging. This will include a "navigational menu", that most readers are using nowadays.  It will output the HTML into separate chapter-files.
• In the Export Tagging  you can also change headings to the corresponding H1, H2 etc. These codes will produce more compatible en more simple/straight CSS. 
• This Split does not work between cover and TOC. You can do this manually in Sigil (an open source epub editor). Just add a paragraph between Cover and TOC
• A lot of css is not working, and this heavily depends on the reader. iBooks is the best, but it also overrules more than others. Examples: color: on a black and white device? Hyphens: iBooks can overrule. Alignment: iBooks can overrule. Margin and font-family: Some readers can overrule, some always overrule. Font-size: can always be overruled. Text-transform, letter-spacing: iBooks can do it,  others don't. A lot of css is not exported by Indesign, because a lot of readers overrule it anyway. So adding it manually in Sigil via CSS edits does not mean it will work, not in all readers anyway.
• Open in iBooks to test.
• Use Kindle Previewer to preview on various Kindles and to convert epub to kindle mobi format. You will need X11 on the Mac, or xquartz  on OS X 10.9 and above:  http://xquartz.macosforge.org/landing/
• Open in Kobo and Nook to test. For these, no Previewers or Emulators are available for Mac, but on Android it is possible.

Workflow

Save a second version of your book, for instance as epub.indd, using all the tips above.

Export to epub, open in Sigil, edit HTML and CSS, save. Then export epub to mobi Kindle.

Future corrections have to be made in both the original.indd as well as in the epub.indd or the HTML-files.