Between 2020.3 and 2021.3 an overhaul of the undo system changed the way Unity creates and processes undo and redo actions. The previous system used snapshots which captured the object at the point of performing undo, which had the side effect of covering up some incorrect uses of the undo system such as child objects and components not being saved to Undo.
In 2021.3 onwards all objects that are expected to be undoable should be explicitly saved into the undo system. The fix seen later in 2022.1 onwards captures the orphaned objects and destroys them for the user as the warning seen in later versions describes. Unfortunately that change is part of another much larger overhaul and would be risky to add to 2021.3 at this point.

A simple work around is to use the undo system as intended and explicitly record the addition of and changes to the child objects being added in the project scripts. The key to this issue is the CanvasRenderer of the ShadowRenderer object being assigned to the CanvasRenderer of the GameObject being deleted by Undo. By using UnityEditor.Undo.RecordObject(renderer, "") directly before the CanvasRenderer is assigned the child object no longer references the deleted object after undoing. See https://docs.unity3d.com/ScriptReference/Undo.html for further details on recording objects correctly within the undo system.