I use multiple pages on many documents. TOC is easier to generate on multiple documents and easier to maintain as a separate document for me. Also chapters in separate documents automatically force a new page for the Chapter which is useful. I only occasionally use book designer as it prefers one file. MobiPocket Creator seems to prefer multiple files particularly to control the location of the generated toc. I have not tried to test the hyperlink problem you experienced. I mostly use ebook publisher for my eb1150 files as it gives me the most control.
Dale
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