When an Automation Process is running, if I make changes manually, for example to change the Status of a Job, will this break the Automation?
No, the Automation Process will continue running and apply the steps.
Note: If you make certain changes while the Process is running, this may affect what data the steps are applied to, depending on what the Process does and what is changed while it is running. For example, if a Process has selected certain Jobs using a view based on a Job's Status, and the Status is changed while the Process is running, the Jobs may already have been selected. So an update may be applied to a Job that was included in a view using the previous Status before it was manually changed.