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This fix assumes you have already followed this guide to create a Unity project for mapping. This way of decompiling the game's assemblies results in having a version of Mirror without any of the Editor utilities, so Networked objects are not automatically given valid scene IDs when you make a custom map. I copied and slightly modified the code Mirror would use to assign scene IDs to work with this specific Unity project setup. Download the script here.
Open your Unity project. In the project window, look in your packages folder for ATLYSS and find the Mirror assembly within it.
Select it, and look in the inspector. Check the "Auto-Reference" box and apply the change.
In your assets folder, create a new folder called "Editor".
Within the Editor folder, import NetworkScenePostProcess.cs.
Unity should automatically compile it. Check the console for any errors. To verify if the script is working, you can duplicate any networked object in your map, save the scene, then close and re-open the scene. Upon re-opening you should see a message in the console the looks like this.
With this script active, you should be able to reuse network objects from any other scene since a new scene ID is created when copied to a new scene. Also, when copying an object from one scene to another, you won't see a console message for a new scene ID since a hash based on scene path already ensures that the IDs will be different. IMPORTANT: If you duplicate a networked object, a new scene ID is not created until you close and re-open the scene, so remember to do that before building your bundles (also save after re-opening).