How to reproduce:
1. Open users attached project
2. Add "GL_Transi_Castle_Hallway01 - stripped" prefab to the scene
3. Press Test > SaveAsPrefabAssetAndConnect

Expected result: The prefab is saved correctly
Actual result: The prefab is broken, with errors specifying that there are duplicate identifiers

Reproducible with: 2019.4.36f1, 2020.3.31f1, 2021.2.14f1, 2022.1.0b12, 2022.2.0a8

Note: The error message will give you the wrong ID due to another bug, you can use "Test -> Find Duplicates" to find the correct duplicated IDs. You can find all the code used in Assets/Editor

Error:
Duplicate identifier -1085746240. File: "Assets/GL_Transi_Castle_Hallway01 - stripped.prefab".
UnityEditor.PrefabUtility:SaveAsPrefabAssetAndConnect (UnityEngine.GameObject,string,UnityEditor.InteractionMode)
PrefabTest:RunPrefabTest () (at Assets/Editor/PrefabTest.cs:19)