When I couldn't figure out how to export the zoo, I tried ringing the entire thing with a barriery and attempting to save that as a blueprint. It would start the process but crash midway through.
That’s a good attempt. In your case it seems to much stuff, I had the same problem.
Split your project in multiple parts and try to use markers in the sky like a pyramid, that are included in each part.
When you replace your stuff, just align those pyramids.
Backup your save, place those markers in the sky.
Delete BCD, but not the markers, build a barrier, make a blueprint. undo undo undo, the same with ACD and so on
EDIT:
This way you can also work around the problem, that you get different stuff saved with habitat-blueprints and regular blueprints. simply use both with this method