Upgrade filebeat and logstash from 5.6 to 6.3

I am trying to upgrade the filebeat and logstash from 5.6 to 6.3, there are two logstash and a lot of filebeat agents, what should do to upgrade smoothly?

I'd do Logstash first and then Beats.

6.3 is EOL though, I would suggest going to 6.8 if you need 6.x. 7.13 is latest.

My arch is filebeat(5.6) -> logstash(5.6) > kafka > logstash(6.3) -> ES(6.3), I think I should upgrade the 5.6 parts first?

If logstash first, is logstash 6.3 backward compatible with filebeat 5.6?

Check out Elastic Support Matrix | Elasticsearch for that.
TLDR yes.

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