If you see a dialog box saying that it wants to replace with another color, then it IS being used.
But sometimes it is not used in an obvious place.
For example, cyan is the color used in Paragraph Shading, and even though you may not have paragraph shading enabled in any paragraph styles, it is technically “burned in” to the Basic Paragraph Style.
So if a paragraph or character or object or table or cell style uses a color (even if it is not applied anywhere), then InDesign gives you that dialog box.

See: https://creativepro.com/picking-the-best-video-format-for-digital-publishing.php

We don’t currently allow uploading of images, so the best option is to post the image somewhere like IMGUR.COM or some other file service and then post the URL here. What you’re looking for sounds pretty complex. Maybe it could be done with a cross-reference. Certainly not with a normal table of contents, I think.

That article you reference is more for setting a particular spacing… not the “best” spacing. See this article for more “real world” suggestions:
https://creativepro.com/what-are-your-favorite-word-and-character-space-settings-for-hjs.php

But it is kind of crazy to try to make justified text where you do not allow any word spacing or hyphenation. The text will look horrible.

David, you are correct that InDesign does not, by default, push CMYK through its color management system to “cross-render” it to the new CMYK. That is on purpose, as most CMYK images are already targeted to a particular output and shouldn’t be messed with. (For example, if I spec 50% cyan in a CMYK image, I don’t want InDesign messing with that… I want it to just pass that 50% through.)

However, you can force cmyk images to be color managed in a couple of ways. You’d have to tell InDesign to honor its embedded profile in Object > Image Color Settings (or on import). And you can also turn off the “Preserve Numbers” feature when creating your PDF. Again, most people should not have to do this, but it can be helpful in certain circumstances.

I talk about this in more detail in my Lynda.com course on color management in InDesign.

By the way, another option might be to export your INDD file as an RGB PDF and then rasterize that by opening it in Photoshop and doing the conversion to CMYK there (if you have to have CMYK). But of course, then you’ll lose vector art.

You could probably use the GREP tab of the find/change dialog box for this. Is it just a single space, or multiple spaces that you want to replace.

Because it is a book, it’s possible that you had reflow in some early chapter which caused one page to be added (if that option is turned on in the book panel’s page numbering options dialog box). Do you have a PDF of the previous version to check page numbers?

I agree that it sounds like a weird mystery. If it were just one file, I’d say maybe something was corrupted and you should do an IDML roundtrip to clear it up. But if this is more than one file, it’s really bizarre.