Java Serialization / Deserialization Duplicate Object Problem

I'm writing a large scale program in java where I keep track of the Nodes with different data structures.

Specifically, one of my Node type have 2 left & right pointers for 2 different Binary Search Trees and I also keep track of that Node in a priority queue.

I have to serialize and deserialize my program to be able to use it for multiple times despite shutdown.

The problem is, when I insert a Node in my program and check the same node in the 3 different structures (2 BSTs and 1 Heap) it's the same exact Node as it should be (I'm using the pointers in the Node to construct BST and it's a part of the heap array).

But whenever I restart my program (serialize / deserilaize) and check the "supposed to be same" Node in the structures, I see 3 duplicates rather than 1 node with the same memory location. My code is definitely creating duplicates while the save/load process.

Here's an outline of my loading (deserilaize) function:

public BSTStructure load() {
        BSTStructure bstStructure = null;
        try {
            File file = new File("filepath");
            boolean fileCreated = file.createNewFile();
            FileInputStream fileInput = new FileInputStream(file);
            ObjectInputStream in = new ObjectInputStream(fileInput);
            bstStructure = (BSTStructure) in.readObject();
            fileInput.close();
            in.close();
            return bstStructure;
        } catch (FileNotFoundException e) {
            System.out.println("filepath file is not found");
        } catch (ClassNotFoundException e) {
            System.out.println("Class not found");
        } catch (EOFException e) {
            System.out.println("file is Empty");
            bstStructure = new BSTSTructre();
        } catch (Exception e) {
            e.printStackTrace();
        }
        return moviesByID;
    }

public void save(BSTStructre bstStructure) {
        try {
            FileOutputStream file = new FileOutputStream("filepath");
            ObjectOutputStream out = new ObjectOutputStream(file);
            out.writeObject(bstStructure);
            out.close();
            file.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

My save/load functions for the other data structures are similar.

I hope that you can help me with this.

I narrowed diwon my problem from a +2000 lines of code to this specific issue.

I can't reproduce the issue unless I restart (save / load) the program.