Repair metal roof boot

I have a metal roof on my cottage. My hot water tank is vented through a rubber boot. The rubber boot is leaking. What is the best way to repair it. If I have to remove the old boot how do I clean the roof of the old silicon without scratching the paint. Can I add more silicon to the existing boot? Thanks.

Personally, I would buy a new star vent with a storm collar and do away with the rubber boot. You can mold the vent to fit the roof. I like geocel or np1 under the base and then field screw it if it’s on a solid deck, or lap screws if it’s not.