I have created an epub in Indesign. That ePub has been converted to a mobi file for kindle readers. Any ideas on how to edit the HTML/CSS of an epub or mobi file created in Indesign to make direct changes such as linking footers and making formatting changes to content?
If you want an easy way to do it, probably the easiest solution is to use the Calibre program. It lets you convert almost any format into an .epub file, which the (separate) Calibre editor can then edit. If desired, you can use Calibre to convert the edited .epub file back to the original format as a final step.
The .mobi format simply can't be edited in any meaningful way, so it's necessary to convert it to .epub, which seems to be the most flexible format of all.
One reason I'm particularly enthusiastic about .epub files is that the Calibre editor has so many tools to automate many functions of editing that type, making it fairly easy to make changes. And the Calibre developer guy is actively making improvements to it all the time.
The editor has a particularly nifty search-and-replace function, and even has a button for checking the .epub file for errors.
The thing to bear in mind is that Calibre is 2 programs, one is a manager program for organising your ebooks regardless of what format they are, and which can convert a book from one format to another (a huge range of different types); and then there's a second, separate program for editing .epub format files.
Calibre's philosophy is that you'll convert your ebook to .epub format, edit it in that format, then convert it back to the original format (though in fact you can choose any output format you favour, from a huge range of choices).
And Calibre's a free program!
It copes with almost any type of ebook, as long as it's not a locked (DRM) format.
An EPub file is a zip compressed container. Just unzip it and you will find the HTML files that you want to edit. You can also use an EPub editor like sigil.