Lets start with the chapters. I can't say about hyperlinks, but inter-file cross-refernces, which are quite similar are very prone to breakage, so the standard advice is to keep the whole book in one file if you need to use cross-references. For safety, save often, and save backup versions.
If you use a SPOT color for your link colors you can use the Ink Manager to alias it to Black (or any other color). This means you can export one PDF in color for the web, and then export a second PDF for print, which you'll want to do anyway since print requires higher resolution, and during the export you can go to the Ink Manager and change your spot blue to black.
You cannot specify that colored text in the PDF will print as black, but your users probably can. Most printer drivers have a "Text as Black" option and Acrobat and Reader have a Print Color As Black option, but that's global, not just text.
Since I don't use hyperlinks in my work at all, and seldom use cross-refs, I'll leave your forward/backward link question for someone else.
Thanks Peter. After another cup of coffee I figured it out.
I learned my lesson abotu having all my eggs in a basket when it comes to file sizes vs. multiple chapters. I err on the side of caution and go with multiple chapters. I've yet to have the cross links fail with the caveat that it takes some doing to not mess then up.
I'm going to explore the spot ink train of thought and see what I come up with. Your suggestion of using two PDFs, one for print and one for online, will probably be the best way to go about it. I had thought that perhaps using variables I might accomplish it, I was wrong as that seems to be for something else entirely.
A. Wayne Webb