I need to understand first what do you mean by removing file beat!!
Possibility-1
if you have uninstalled and installed again, then obviously file beat will read the data from the path again(which you have re-ingested and post it to logstash->elasticsearch->kibana(assuming old data is not been removed from elastic node) hence the duplicates.
Possibility-2.
You just have stopped filebeat,configured for logstash and restarted filebeat and may be your registry file is not been updated properly during shutdown(as you know,file beat reads line by line and update the registry file upto what line it has successfully published to logstash/elasticsearch/kafka etc and if any of those output servers face any difficulty processing huge load of input coming from filebeat then filebeat waits until those servers are available for further processing of input data.Once those output servers are available,filebeat reads the registry file and scan upto what line it has published and starts publishing next line onwards).
Sample registry file will be like
{
"source": "/var/log/sample/sample.log",
"offset": 88,
"FileStateOS": {
"inode": 243271678,
"device": 51714
},
"timestamp": "2017-02-03T06:22:36.688837822-05:00",
"ttl": -2
}
As you can see, it maintains timestamp in the registry file.
So this is one of the reasons for duplicates.
For further references, you can follow below links
https://discuss.elastic.co/t/filebeat-sending-old-logs-on-restart/46189
https://discuss.elastic.co/t/deleting-filebeat-registry-file/46112
https://discuss.elastic.co/t/filebeat-stop-cleaning-registry/58902
Hope that helps.