test/Assets/Editor/PrefabApplyOverrideShortcut.cs

using UnityEditor;
using UnityEditor.ShortcutManagement;
using UnityEngine;

public static class PrefabApplyOverrideShortcut
{
    private const string MenuPath = "Tools/Prefab/Apply Overrides %#a";

    [MenuItem(MenuPath)]
    private static void ApplyOverridesFromSelection()
    {
        var selectedObjects = Selection.gameObjects;
        if (selectedObjects == null || selectedObjects.Length == 0)
        {
            Debug.LogWarning("No GameObject selected.");
            return;
        }

        int appliedCount = 0;
        foreach (var selectedObject in selectedObjects)
        {
            if (selectedObject == null || !PrefabUtility.IsPartOfPrefabInstance(selectedObject))
            {
                continue;
            }

            var rootInstance = PrefabUtility.GetOutermostPrefabInstanceRoot(selectedObject);
            if (rootInstance == null)
            {
                continue;
            }

            PrefabUtility.ApplyPrefabInstance(rootInstance, InteractionMode.UserAction);
            appliedCount++;
        }

        if (appliedCount == 0)
        {
            Debug.LogWarning("Selected object(s) are not prefab instances.");
            return;
        }

        Debug.Log($"Applied prefab overrides for {appliedCount} instance(s).");
    }

    [MenuItem(MenuPath, true)]
    private static bool ValidateApplyOverridesFromSelection()
    {
        var selectedObjects = Selection.gameObjects;
        if (selectedObjects == null || selectedObjects.Length == 0)
        {
            return false;
        }

        foreach (var selectedObject in selectedObjects)
        {
            if (selectedObject != null && PrefabUtility.IsPartOfPrefabInstance(selectedObject))
            {
                return true;
            }
        }

        return false;
    }

    [Shortcut("Prefab/Apply Overrides", KeyCode.A, ShortcutModifiers.Action | ShortcutModifiers.Shift)]
    private static void ApplyOverridesShortcut(ShortcutArguments _)
    {
        ApplyOverridesFromSelection();
    }
}