When you deploy on new versions you can see this deprecation:
W0723 20:57:03.499655 2113 prune.go:71] Deprecated: kubectl apply will no longer prune non-namespaced resources by default when used with the --namespace flag in a future release. To preserve the current behaviour, list the resources you want to target explicitly in the --prune-allowlist flag.
This is not an issue right now, but it should be fixed for the future.