We've had some link issue too when converting from Word to PDF.
We have 2 fairly large files - one ebook worked fine and the other has problems.
And they are roughly the same size, type, and layout too.
Simple written out links
www.somesite.com are fine but when we use affiliate links
www.oursite.com/product.html they work in one ebook and not in the other.
Yeah they are cut off at the "/" in the link.
Very mysterious!
We've tried the free trial of Adobe Acrobat plus virtually every PDF maker on the planet...