Fix fileId in asset file. May be useful if you change type of field and Unity doesn't fix references. Make sure to change regex pattern for your needs.

ReferenceFixTool.cs

using UnityEngine;
using UnityEditor;
using System.IO;
using System.Text.RegularExpressions;

public class ReferenceFixTool
{
    [MenuItem("CONTEXT/ScriptableObject/Fix References")]
    static void FixReferences(MenuCommand command)
    {
        ScriptableObject obj = command.context as ScriptableObject;
        Debug.Log($"Fixing references for {obj.name}");
        var contextAssetPath = AssetDatabase.GetAssetPath(obj);
        Debug.Log($"Open scriptable object at path: {contextAssetPath}");
        var inputStringStream = new StreamReader(contextAssetPath);
        var outputStringStream = new StringWriter();
        while (!inputStringStream.EndOfStream)
        {
            var line = inputStringStream.ReadLine();
            var match = Regex.Match(line, @"prefabRef: \{fileID: ([-0-9]*), guid: ([a-z0-9]*)");
            if (match.Success)
            {
                var assetPath = AssetDatabase.GUIDToAssetPath(match.Groups[2].Value);
                Debug.Log($"asset path: {assetPath}");
                var asset = AssetDatabase.LoadAssetAtPath<GameObject>(assetPath);
                if (asset)
                {
                    AssetDatabase.TryGetGUIDAndLocalFileIdentifier(asset, out string _, out long localId);
                    line = line.Replace(match.Groups[1].Value, localId.ToString());
                    Debug.Log($"Output line: {line}");
                }
            }

            outputStringStream.WriteLine(line);
        }
        inputStringStream.Close();
        File.WriteAllText(contextAssetPath, outputStringStream.ToString());
        AssetDatabase.Refresh();
    }
}