Getting MissingReferenceException from the component pool when I destroy a spline

[_Aka_]

As for the shapes along the spline, I didn't explain properly, I'm trying to extrude along the spline, but change the size & shape of the extrusion as I go.  I will be roughly circular.  Ideally I'd like to be able to vary the mesh geometry along the length of the spline, including adding noise and adjusting the number of radial segments, but I understand if that's beyond the scope of this plugin.

Changing the size of the extrusion's shape is doable here.
Changing the actual shape of the extrusion is doable with this module. It is used in example scene 27_CGVariableExtrusion

The error is coming from Assets/Plugins/DevTools/Components/ComponentPool.cs:318, so it's not really my code that's throwing the error, which is why I decided to ask about it.

Of course, I am not saying the opposite. But still I have to ask you questions to know how to reproduce the bug in order to fix it. Your use case seems very particular, since I am not aware of any other user having your issue.
After reading your code, I can confirm my earlier guess, which is that you are destroying objects twice. You do not need to destroy the children, since destroying the parent will lead to the destruction of the children: "If obj is a GameObject, it destroys the GameObject, all its components and all transform children of the GameObject" from https://docs.unity3d.com/ScriptReference/Object.Destroy.html
In conclusion, avoiding the destruction of a spline twice will avoid the raise of the exception.
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