Export an alternate layout from a indesign book

Hello,
I'm working on a big file, which has been, for size reasons, separated in multiple files that have then been assembled in an indesign book
Problem: This document is edited for print and also as an interactive pdf for ipad, which is why I have created an alternate layout for the ipad version, which contains a navigation based on hyperlinks, linking different pages and documents from the Book.
But here is the thing, when exporting the whole book to pdf (using the Indesign Book panel), I can't choose the layout I want to export, as I can do when I export from a single document with several alternate layouts
What I get when I export from a single file with two alternate layouts to interactive pdf
What I get when I export the Indesign Book with two alternate layouts to an interative pdf
Why is that? Is there a way I can export only one layout without having to RE-assemble the whole document into one file?
If I export the whole book as it is, my two alternate layouts are just following each other and it's a big mess, not to mention the hyperlinks don't work anymore.
Also, if the only way is to make one file, the file is then too heavy to be worked with, it's 280 pages long, with HD images on every page ( and the alternate layouts double the pages...)
Does anyone have a solution?

You mean, breaking the document into two or three files and then exporting each of these and then assembling the pdf files?
But then the hyperlinks from one doc to another don't work. I tried it already.
The problem is that I need to export ALL of these documents into ONE pdf because of the interactivity of the hyperlinks.

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Export an alternate layout from a indesign book

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