Thanks for your response and apologies for the delay in answering. The latest versions of InDesign and Acrobat take care of some of the issues. Export to fixed layout epub now retains formatting (including sidebars in the margins) and Kindle Create does a pretty good job of taking the PDFs and converting to Kindle files, but all the files need to be in the same PDF or indd file to allow links between chapters of the document.

Right now, I’m trying to figure out the best way to manage combining files rather than using separate PDF files in the same directory on a users’ hard drive.

Currently, each chapter is a separate INDD file and those indd’s have been group into ID books. Page numbering is important and styles are not entirely consistent between books, but can be reconciled. Here’s my first issue:
1. Do I move individual indd files into one big book? Can I merge separate books into one master book and which would be the best way?
2. Hyperlinks in the current setup go to different books/indds and with export to PDF, those links break. Is there a script or batch process to convert links to other indd files to the big master file?
3. Alternatively, do I export all the individual indd files to separate PDFs and then combine to a PDF portfolio or binder?

This project took two years to build and I don’t want to spend another two years to use current technology. If you’re interested I can send you a few sample chapters so it’s clearer. I used ID publish online to try a section at https://indd.adobe.com/view/eb6dc565-a5c4-4ede-9862-cc154fd8901f

Any thoughts welcomed.