Fleet Managed Pipelines and Indexes

I have the integration for Nginx installed on my cloud deployment, monitoring and ingesting logs from a container deployment of the Nginx proxy. The integration for Nginx appears to be looking for an access log format that is very different from the one that the deployment in the container is producing.

I wanted to write my ingest pipeline to match the format I see coming into the deployment, but I don't want to cause conflicts with the fleet managed indexes or ingest process. How is this traditionally addressed? I suppose I could remove the integration and create a custom log integration instead but I think that the other log format (for error logging) is correct and working.

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