Hi Guessed, thank you for your answer.
While the protection features is useful on its own right, it did not solve the issue.
When I drag a protected custom shape in my document, its properties are still changed, but with protection active, I cannot change the protected properties manually.
I have made an additional observation: when I drag the shape in the document (it represents a valve, so I will call it "valve shape"), select and copy it, then create a new custom shape, edit that, and select paste, the valve shape appears with the correct colors.
That looks like as if the document applies some kind of default settings to shapes that are copied from the ciipboard or dragged from a stencil. I will look into "default formats of a document" closer.