You can remove agent machines from the cluster during a build without requiring downtime or disabling Agents in the Cluster Manager, with the following advisories:
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If possible, shut down Agents before rebooting agent machines. Not shutting down Agents before a reboot might cause commands to fail unexpectedly, which could manifest in spurious build failures.
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After rebooting, agent machines that automatically start Agents will connect to the Cluster Manager and will be assigned builds and so on.