Hi ASCR0001,
I also had a strange problem with fonts on my ibook project as I didn't know about these limitations. In my case, I had installed a custom font. I looked at my iBA and found that Lucida Grande doesn't appear in the font tool, but that font is readily available in, say Pages, TextEdit, etc. So, perhaps at one time you had imported or copied and pasted some text into iBA, changed it to something else, and now you can't find any trace of Lucida Grande. But it may still be there, for example, in a blank line, a space in a paragraph, hidden in a gallery caption, or some obscure place.
I resolved my font error by exporting each chapter out of iBA and into Pages, then selected the entire content, changed the font (lately I'm using Avenir) and then I copied it from Pages and pasted it back into a fresh chapter in iBA. Galleries could be dragged and dropped into the new chapter, but I chose to rebuild those instead.
This took a lot of time but had to be done. Older iBook Author guides had erroneously indicated that any font could be used, but that hasn't been true in the recent past. The key thing I learned was that any font used in iBA must be an iOS font, too. My Mac has many non-iOS fonts, so I have to be careful.
I hope this helps you get your iBook finished. Good luck and Best Regards,
John