It is very hard, but here my steps to sav as much as possible.
First place some markers , like pyramids, in the air above every habitat. save the habitats as blueprint
Next step: mutliselect the entire zoo ( or if it is to much, stuff sections) including the pyramid-markers and save it/them as regular blueprint.
Remove the habitat, or at least the doors. create a big habitat around the zoo, or the stuff you need. Save this again as habitat.
Why these steps... blueprints as habitat save the terrain, but not every construciton piece. The regluar blueprints save every construction piece but not terrain.
In your new zoo, reconstruct slowly. Take the pyramids as anchorse that cover each other, to get the right positions.
To much work?
Yes...and you still loose your paths...and in many cases you wont be able to recreate them....So maybe start a new one