My best guess is that the process conditions are not 'normal' during startup of a plant, process or unit.
So, some of the interlocks, alarms or permissives that are built into the PLC, DCS or hardwire control logic will need to be bypassed or overridden during startup, and then placed back into service once the unit is up and running.
Your company/plant should have a process for such things. Operations needs to be aware of what is overridden before they start and while they are running. The engineer or technician should be very explicit in what work is being performed (or that the process is in startup), and Operations needs to sign each item on the override list and it should be posted. Each item should also have a maximum time that it can be overridden. It can be on a simple excel spreadsheet.
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This is normally the space where people post something insightful.