I think that now I understand what happened. My expectation about patching system behavior when component is transitive was wrong. During patch application, transitive component condition gets evaluated and, if it has changed from true to false, component gets deleted. However, to facilitate patch removal (which means that deleted component must be restored), the system doesn't cache the component somewhere. The patch that deletes the component cannot be removed in every case, without access to the original MSI. In one case when I had patch removal appear to restore the deleted component, it was because I have already patched the component once before its removal. So it existed in baseline cache and original MSI was not needed.
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