Elastic Agent manages and starts the beats on your behalf, you do not need to manage them or control them.
On upgrade the Elastic Agent will upgrade the beats, if it hits an issue with upgrading it will automatically rollback to the previous version of the Elastic Agent and beats. The beats and Elastic Agent are in alignment with versions. So updating Elastic Agent updates the underlying beats, same with rollback (beats rollback).
On upgrade the beats are stopped for a moment in time to perform the upgrade. That does mean there is a chance of data lost during that time. When it comes to logs the last read log line is stores so on start of upgrade version it picks up where it left off. In the case of metrics there is a possibility of a hole in the data while it performed the upgrade.
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