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Is there a way to tell bacula to stop queuing new jobs from the schedule, but finish the ones that are currently running?

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I believe it is this command you're looking for in bconsole:

disable job <job-name>

This command permits you to disable a Job for automatic scheduling. The job may have been previously enabled with the Job resource Enabled directive or using the console enable command. The next time the Director is restarted or the conf file is reloaded, the Enable/Disable state will be set to the value in the Job resource (default enabled).

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