Handling Kuberenets Labels Mapping Conflict

I have two kinds of labels which are causing a mapping conflict:
app: * vs. app.kubernetes.io/instance: *
(type text vs. type object)
The second label is predefined by Kubernetes and is used to differentiate between different instances of the same applications whereas the first one isn't.
In my flow, Logstash is pulling messages from Kafka and export them directly to ES.
I know this issue is handled out-of-the-box in Filebeat (by dedot:true), and i wonder how the community handles this without using Filebeat since it's a common use-case.

failed to parse field [involvedObject.labels.app] of type [text] in document with id '***'. Preview of field's value: '{kubernetes={io/instance=*}}'"

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