I am currently working on a similar project. I follow these steps:
1. Export from InDesign to PDF.
2. Open PDF in illustrator.
3. Go over all of the pages, convert groups to layers by choosing from the flyout menu – release to layers.
4. have all layers one above each other rather than nested.
5. Export each illustrator file seperatly with PDF compatibility checked.
6. Import them in AE
7. Create a large comp and place the files together.
8. Use the pan behind tool to provide the right folding axes.
9. Use Y rotation to fold.
If you have multiple pages together, precomp, reduce the size of the comp duplicate and place layers to get seperate comps.
This allows for both folding AND some sophisticated animation using the existing illustrator layers..
Hope this helps,
Amit