I am using BDX (Blender with libgdx engine) to create my game. I am not sure on how to implement 3D path finding using A* search. I looked into gdx-ai, but that is for 2D.
Having used A* path finding algorithms previously, my advice would be to take your Terrain, and break it down into smaller rectangles. Run a check to see if any of these rectangles co-inside with collidable entities. If they do, mark them as solid. From there, ensure each rectangle has a node, and continue as you would for calculating with 2D A*.
When it comes to Y: This depends on how you have implemented the floor/terrain. Personally, I just set Y to be the height of the terrain at the current point. This works fine for me.
If you are also unfamiliar with A* path finding in 2D, there is a really good game dev series by TheCherno on YouTube that covers this which i'd advise looking at.
Hope that helps!