I have a Logstash(6.8) configured with more than one conf files using one pipeline. when i execute the logstash, it is collecting logs from all inputs and sending it to all output Elastic Search index configured in pipeline conf.
That sounds like it is working as expected. Events from all the inputs in a single pipeline are sent to all of the outputs. If you want the configuration files to be independent then use pipelines.yml to run each in its own pipeline.
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