Fully break prefab connection so it can't be reconnected. Just put into an Editor folder and you'll find the menu option "GameObject/Break Prefab Instance Permanently"

BreakPrefabPermanently.cs

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

public class BreakPrefabPermanently
{
    [MenuItem("GameObject/Break Prefab Instance Permanently", priority=100)]
    static void BreakPrefab()
    {
        GameObject prefab = PrefabUtility.CreatePrefab("Assets/BreakPrefab.prefab", Selection.activeGameObject);
        PrefabUtility.ReplacePrefab(Selection.activeGameObject, prefab, ReplacePrefabOptions.ConnectToPrefab);
        AssetDatabase.Refresh();
        AssetDatabase.DeleteAsset("Assets/BreakPrefab.prefab");
        PrefabUtility.DisconnectPrefabInstance(Selection.activeGameObject);
    }

    [MenuItem("GameObject/Break Prefab Instance Permanently", validate = true)]
    static bool BreakPrefabValidate()
    {
        return Selection.activeGameObject;
    }
}