Moving to Kobo from Amazon, which file format should I use?

[DNSB]

Originally Posted by Aleron Ives

I've also found that the footnotes popup almost never works with KEPUB. Footnotes appear to be the bane of e-books. x)

You might want to check the size of the footnotes files. There is a limit on the number of characters allowed. You might also want to make sure that the epub:type="footnote" or epub:type="endnote" is used. The Kobolabs epubspec github page has more on this. Partial quote below:

Warning: Hyperlinked content not using the epub:type attribute footnote or endnote will display as a pop-up on Kobo's iOS and eInk platforms in cases where all the following criteria are met.

The link references a location in the EPUB and also references a specific node within the HTML. Ex.
<a href="chapter.html#uniqueID">link text</a>
Where chapter.html is a file within this EPUB and where uniqueID is the id of a node within that html document.

The content in the node is nine characters or more once stripped of the HTML tags. Ex.
<p id="uniqueID">123456789</p>

The node being linked to is less than or equal to 5000 characters.

The location being linked to comes after the location being linked from. Ex. A reference in Chapter 2 links to a location at the end of the file titled Endnotes or a reference at the beginning of Chapter 2 links to a location at the end of Chapter 2.

In the last while, I haven't had issues with footnotes/endnotes when I follow the rules.