It is currently returning bad access errors.
Then that's what you should worry about as your first priority. That's a serious bug.
From what I can tell, it looks like I am inserting a pointer to a temporary object, temp_node, and temp_mesh.
This aren't "temporary" objects, that means something different (why do you keep using "temp" in your variable names?), but you're right about the problem:
shared_ptr<ofMesh> shared_mesh(&temp_mesh);
This creates a shared_ptr which owns the pointer &temp_mesh and so will delete it when there are no more shared_ptr objects that share ownership of that pointer.
But that pointer is the address of an automatic variable (aka stack variable) which goes out of scope at the end of the block. You don't "own" that object, the block scope of that function manages it automatically. If you don't own it then you can't give ownership of it to the shared_ptr, because it's not yours to give away.
When the scope ends the automatic variable temp_mesh will be destroyed automatically, but there are still shared_ptr objects that hold that pointer, thinking they own it. When you try to access the object through those shared_ptr objects you access a destroyed object, after its lifetime has ended. Then when there are no more shared_ptr objects that own the pointer it will be deleted, but it wasn't created with new so that's a serious bug. (You get this right in the other function, so I'm not sure why you've done it wrong in setupMesh).
If you want a shared_ptr to own an object you need to create it with new, or preferably create it with std::make_shared: *
shared_ptr<ofMesh> mesh = std::make_shared<ofMesh>();
mesh0->setMode(OF_PRIMITIVE_LINE_STRIP);
mesh->setupIndicesAuto();
mesh->addVertex(root->location);
mesh->addColor(ofColor(0));
meshes.push_back(shared_mesh);
checkChildren(root, mesh.get());
This creates an object that is owned by a shared_ptr right away, so there's no problem of transferring ownership of something that can't be owned by a shared_ptr.
* Or you can use a "null deleter" but that's way too advanced for this answer, and won't make it OK to use automatic variables like this.
