William C. answered 09/09/21
Expert Tutor for Math, Science, Computer and Test Prep
Your best bet is probably Adobe InDesign.
Word gets wonky after a few hundred pages. I have published books with extensive footnotes, but these are typically a compilation of articles placed into a single document.
In that case, all of the references are correct, since I am adding them to one continuous document. It appears you are doing this in the other direction.
You could try to embed an Excel worksheet that has these connections at the end of your book, or include it in each book. That way, the hyperlinks will connect to your content.