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If the agents haven't checked in for over 45 days, the license seat is already freed up for use with other machines. If you no longer want the agent installed, you can actually send the command to uninstall the agent from the console by going into Machine View or Manage > Agents, then select the machines you wish to uninstall the agent from, right click, and choose Agents > Uninstall. As long as the console can successfully contact the agent it should remove it.
If the agent machines in question have not checked in for more than 45 days, and those same machines have not received an agentless deployment during said time, the license seats will have been automatically freed.
You can certainly delete the machine records from the database if they are no longer pertinent. Simply refresh the Machine View, select the machine listing or listings in question, then select 'Delete' from the alternate (right-click) menu. This will remove all record of said machine from the database, and will cause the console to initiate an uninstallation of the agent software the next time the machine attempts to check-in (e.g. the agent will be considered 'unregistered' with the console).