HierarchyWindowHelper.cs

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

class HierarchyWindowHelper
{
    private SerializedObject so;

    private SerializedProperty expandedIDsProperty
    {
        get
        {
            return so.FindProperty("m_TreeViewState.m_ExpandedIDs");
        }
    }

    public HierarchyWindowHelper(EditorWindow hierarchyWindow)
    {
        so = new SerializedObject(hierarchyWindow);
    }

    public List<int> GetExpandedIDs()
    {
        so.Update();
        var expandedIDs = new List<int>();
        for (int i = 0; i < expandedIDsProperty.arraySize; i++)
        {
            expandedIDs.Add(expandedIDsProperty.GetArrayElementAtIndex(i).intValue);
        }
        return expandedIDs;
    }

    public List<string> GetExpandedNames()
    {
        return GetExpandedIDs()
            .Select(expandedID => EditorUtility.InstanceIDToObject(expandedID))
            .OfType<GameObject>()
            .Select(gameObject => GetAbsoluteGameObjectName(gameObject.transform))
            .ToList();
    }

    private string GetAbsoluteGameObjectName(Transform transform)
    {
        if (transform.parent)
        {
            return GetAbsoluteGameObjectName(transform.parent) + "/" + transform.name;
        }

        return transform.name;
    }

    public void SetExpandedNames(List<string> expandedNames)
    {
        var expandedIDs = expandedNames
            .Select(expandedName => GameObject.Find(expandedName))
            .Where(gameObject => gameObject != null)
            .Select(gameObject => gameObject.GetInstanceID()).ToList();

        SetExpandedIDs(expandedIDs);
    }
    public void SetExpandedIDs(List<int> expandedIDs)
    {
        so.Update();
        expandedIDsProperty.ClearArray();
        expandedIDsProperty.arraySize = expandedIDs.Count;

        for (var i = 0; i < expandedIDsProperty.arraySize; i++)
        {
            expandedIDsProperty.GetArrayElementAtIndex(i).intValue = expandedIDs[i];
        }

        so.ApplyModifiedProperties();

        Reload();
    }
    public void Reload()
    {
        var methodInfo = so.targetObject.GetType().GetMethod("ReloadData", BindingFlags.Instance | BindingFlags.Public);
        methodInfo.Invoke(so.targetObject, new object[0]);
    }
}

NewBehaviourScript.cs

 [MenuItem("TestMenu/Build")]
    static void Buid()
    {
        var type = Types.GetType("UnityEditor.SceneHierarchyWindow", "UnityEditor.dll");

        // 特定のHierarchyウィンドウを取得する
        var hierarchyWindow = EditorWindow.GetWindow(type);


        HierarchyWindowHelper hierarchyWindowHelper = new HierarchyWindowHelper(hierarchyWindow);

        // ExpandedNames を取得する
        var expandedNames = hierarchyWindowHelper.GetExpandedNames();
        
        BuildPipeline.BuildPlayer(new string[0], "Test", BuildTarget.WebPlayer, BuildOptions.None);

        // ExpandedNames を設定する
        hierarchyWindowHelper.SetExpandedNames(expandedNames);
    }