One way I've gotten around this problem is to lay everything in
Illustrator out in a big spread, rather stacking content in layers. I
then place this file into multiple content boxes in InDesign, panning
and zooming to the appropriate locations.
Using Illustrator and InDesign together for design documentation is
often more trouble than it's worth, and I agree that you may want to
check out some other tool options. That said, I hope the solution I
mentioned is helpful!