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Would it be possible for me to create 2 separate functionapps - 1 dedicated to executions on the control queues, the other dedicated to executions on the work item queue?

This is not possible today because each instance of your app will always try to read from both the control queue(s) and the work-item queue. The only time an instance will read from just the work-item queue is if it can't acquire a partition, but even this condition is potentially transient. This is something we'd like to change in the future, but we haven't had a chance to work on this yet.

For now, if you have a strong need to separate your orchestration instances from activity instances, the best practice would be t…

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