GameDataController.cs

using System.Collections.Generic;
using System.Linq;
using UnityEngine;

public class GameDataController : MonoBehaviour
{
	public static SaveData saveData;

	private void Awake()
	{
		LoadData();
	}

	[ContextMenu("Save Data")]
	public void SaveGame()
	{
		var data = JsonUtility.ToJson(saveData);
		PlayerPrefs.SetString("GameData", data);
	}

	[ContextMenu("Load Data")]
	public void LoadData()
	{
		var data = PlayerPrefs.GetString("GameData");
		saveData = JsonUtility.FromJson<SaveData>(data);
	}

	private void OnDisable()
	{
		SaveGame();
	}

	public static bool GetState(MagicCube magicCube)
	{
		if (saveData.magicCubes == null)
			return false;

		if (saveData.magicCubes.Any(t => t.id == magicCube.name))
			return saveData.magicCubes.FirstOrDefault(t => t.id == magicCube.name).isRed;

		return false;
	}

	public static void SetState(MagicCube magicCube, bool isRed)
	{
		if (saveData.magicCubes == null)
			saveData.magicCubes = new List<MagicCubeData>();

		var magicCubeData = new MagicCubeData() { id = magicCube.name, isRed = isRed };
		saveData.magicCubes.RemoveAll(t => t.id == magicCubeData.id);
		saveData.magicCubes.Add(magicCubeData);
	}
}

MagicCube.cs

using UnityEngine;

public class MagicCube : MonoBehaviour
{
	public bool IsRed { get; set; }

	private void Start()
	{
		IsRed = GameDataController.GetState(this);
		UpdateColor();
	}

	private void Update()
	{
		if (Input.GetButtonDown("Fire1"))
		{
			Ray ray = Camera.main.ScreenPointToRay(Input.mousePosition);
			RaycastHit hitInfo;
			if (GetComponent<Collider>().Raycast(ray, out hitInfo, Mathf.Infinity))
			{
				IsRed = !IsRed;
				UpdateColor();
				GameDataController.SetState(this, IsRed);
			}
		}
	}

	private void UpdateColor()
	{
		GetComponent<MeshRenderer>().material.color = IsRed ? Color.red : Color.green;
	}
}

SaveData.cs

using System;
using System.Collections.Generic;

[Serializable]
public struct SaveData
{
	public int currentHealth;
	public int lastLevelBeat;

	public List<MagicCubeData> magicCubes;
}

[Serializable]
public struct MagicCubeData
{
	public string id;
	public bool isRed;
}