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5. Now, would he have removed the leads from the transformer and grounded the cables? Or would he have not dis-connected the leads and grounded the transformer leads with the HV cable attached?
6. Is it proper protocol to ground the secondary also?
Temporary grounds are required when it is possible that a voltage could reappear at the point of work. If there are cables connected that can have voltage induced on them or if they could be connected to another source, then they should be grounded before working on them. This needs to be established by company safety procedures. Often procedures call for grounding all MV and HV equipment while working on it.
It is probable that once the single feed cable capacitance was discharged, no voltage could appear. If you have the temporary ground set there, I would recommend connecting it to the primary while the work is being performed, even if the cable is in a location where no voltage can be induced on it.