Upgrade ElasticStack from 2.X to 5.4.3-1 not showing old logs

EDIT: looking through the documentation some more, it looks like I should have used the migration tool to reindex when I was still in verison 2.4.5. Is there any way to do this after already upgrading?
The migration helper says it will run on Elasticsearch versions 2.3.x and 2.4.x only.

I just upgraded to the newest version of Elastic Stack. New data is coming in from all my machines but now I do not have access to any of the data from before the upgrade.

The old versions I upgraded from were:
Elasticsearch 2.4.5
Kibana 4.5.4
Logstash 2.3.4

and they are now all at 5.4.3-1.
I read through the breaking changes but didn't see any instructions for importing data from older versions.
Is it possible to integrate the old data into the new version of Elastic Stack?

Is there anything in the logs that might explain what is happening?

It appears to have resolved itself... I can now see all the past logs in Kibana.

EDIT: It appears Kibana version 5.4.3 cannot access the old logs. Updating to Kibana 5.5.0 allows me to see old logs, but Wazuh does not have a compatible plugin for Kibana 5.5.0

EDIT2: It looks like wazuh is working on getting their plugin working with 5.5.0 within the next day or two.

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