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Can't give a definitive answer, but my gut feeling is that welding a smaller bolt to the head of an otherwise perfectly good head bolt would be an ok thing to do.
Taking them out one at a time would also (probably) be ok. I don't think I would take all three out at the same time, though.
You will also have to partially drain the coolant to a level below the lowest bolt thread in the head face.
Mart.