I've moved your question to the InDesign EPUB forum for best results.
Just for reference, you're using the latest update of InDesign CC 2014.2, the February 2015 release? And are we talking about reflowable EPUB or Fixed Layout EPUB?
Thanks, Steve! I previously got zero results in the InDesign EPUB forum, so I had hoped to cast my net wider.
I've been using Adobe InDesign CC 2014 10.1.0.70 x64 Build on Windows 7 but I just updated to 10.2.0.69 tonight and will try again.
More detail: these are all reflowable EPUB, none are fixed layout. I'd be happy to upload content if that's both helpful and permissible.
I've tried again with 10.2.0.69 on a book that in previous versions produced the consistent output I've come to rely on.
The output now has <span class="CharOverride-2">...</span> meaning bold in some files and italic in other files within the same epub.
Each file now has two stylesheets:
<link href="../Styles/idGeneratedStyles_0.css" rel="stylesheet" type="text/css" />
<link href="../Styles/idGeneratedStyles_N.css" rel="stylesheet" type="text/css" />
Where N is a stylesheet specific to each document in the book. (Previously, there was just one stylesheet for the whole book.)
Do you use bold or do you use a character style with bold font? Same question with Italic?
How is your Character Style defined? With tags for EPUB and HTML included? Du you use em and strong tags? You should.
Do you have any manual overrides on your text? Avoid it, use a document profile which will show you any occurrence in your document.
This is a good tip.
When I first encountered this new behavior, I did add a new character style called "Italic" and one called "Bold." I set each to the corresponding tags of em and strong. Aside from the oddity of <em class="Italic"> and <strong class="Bold"> this does seem to present a significant improvement.
However, the character styles are obviously not applied when I place a story that has bold and italic in it or when I change to italics on the fly (using keyboard shortcuts). Am I correct in understanding that I need to go back through all documents to replace italics with "Character Style: Italic" and bold with "Character Style: Bold" throughout the book?
Also, I'm good with changing this process for books going forward, but I'm wondering what the simplest way to update past books will be. (They only change in response to errata, and that will happen semiannually at most.)
You can make these change with find & replace.
You can adapt the installed example script with its list to automatize it to an one-klick event. (And include other must be done repairs.)