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This seems like a basic question but I haven't been able to find an answer googling around.

How does scale sets know that a particular VM has finished what it's doing and is able to be de-provisioned?

From the scale sets FAQ the VMs with the highest IDs are removed first. It doesn't say anything about whether it is mid-task or not.

This is important for my application because my tasks are long running (about 30 minutes on a 1CPU/4GB machine).

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To answer my own question, this is called "instance protection" and seems to be a common thing for long running operations.

Scale set instance protection

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