Multiple pipelines output to one cluster - only one of them picks up logs

Elastic Stack Logstash
3

Thanks for the reply.

My pipelines.yml file is the default one, I haven't touched it.

- pipeline.id: main
  path.config: "/etc/logstash/conf.d/*.conf"

As for my pipelines, I can't really share them since they are on a private network, however the general idea is:
pipeline 1: 

input {
    file{
        ...pick up local files...    
    }
}

filter{
    multiple filters{
     ....
    }
}
output{
    elasticsearch{
        hosts => ["es_node"]    
        index => "index-1"
    }
}

pipeline 2: 

input {
    http{
        ...get logs via http...
    }
}

filter{
    different filters{
     ....
    }
}
output{
    elasticsearch{
        hosts => ["es_node"]    
        index => "index-2"
    }
}

Logstash output is normal without errors

...
[main] Pipeline started {"pipeline.id"=>"main"}
...
 Successfully started Logstash API endpoint {:port=>9600}

I hope this is enough information...