How do I handle the existing screws when replacing flashing on a metal roof?

Just had our on-demand water heater replaced. A few days later, I noticed rain leaking around the vent pipe in the attic. The vent pipe has flashing installed on the metal roof, similar to the pic below. It looks like there's a small tear where it seals to the pipe and in general just looks like it's deteriorated a bit. I'd like to replace it with a similar flashing but I'm not sure how to handle all of the screws that were installed around the existing flashing. If I back those out, what must I do to ensure no leaking around them when they are removed? How do I make sure I don't reuse a hole by accident or insert a new screw too close to an existing hole and cause a tear in the metal roof?