FindProblematicAsset.cs

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

public class FindProblematicAsset
{
    [MenuItem("AssetDatabase/ZeroGUID")]
    public static void GetZeroGUID()
    {
        var allFiles = Directory.EnumerateFiles("Assets", "*").ToArray();
        var allAssets = new HashSet<string>(AssetDatabase.GetAllAssetPaths());

        for(int i = 0; i < allFiles.Length; ++i)
        {
            //Make sure we have forward slashes only
            var curFile = allFiles[i].Replace(@"\", "/");

            //Ignore .meta files as they're not part of AssetDatabase.GetAllAssetPaths();
            if (!curFile.EndsWith(".meta") && !allAssets.Contains(curFile))
            {
                Debug.Log($"File path is in project, but not found inside AssetDatabase: {curFile}");
            }
        }
    }
}