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Related issues: * https://github.com/kubernetes-sigs/kustomize/issues/5031 * https://github.com/kubernetes-sigs/kustomize/issues/5171 After noting this behaviour was not present ind89b448c74a `git bisect` pointed to the change1b7db20504. The issue with that change is that upon seeing a `null` node it would replace it with a node whose value was equivalent but without a `!!null` tag. This meant that one application of a patch would have the desired approach: the result would be `null` in the output, but on a second application of a similar patch the field would be rendered as `"null"`. To avoid this, define a new attribute on `RNode`s that is checked before clearing any node we should keep. The added `TestApplySmPatch_Idempotency` test verifies this behaviour. See also https://github.com/kubernetes-sigs/kustomize/pull/5365 for an alternative approach