If you have the full version of Acrobat, you can join PDFs together into one PDF. I suggest you output your book in sections. Some sections will work, and others won't. If your book is 64 pages, try 1-32 then 33-64. If 1-32 doesn't work, try 1-16 and 17-32. If 17-32 doesn't work, try 17-24 and 25-32. Eventually, you will find which pages won't output, and then you can look on those pages to try to find out what is causing it. Sometimes it's a bad font or a bad image. Sometimes the document has corruption (see this link to fix minor corruption).
In the end, you may fix all the problems and get back the ability to PDF the whole document in one go, but this method may get you a PDF that you can use sooner than later.