what is the best and safest way to remove old silicone from metal yoyos without scratching the yoyo.

Just use a needle to pick it out. You have to use some force to scratch it, depending on the coating. A scratch in the response recess shouldn’t be a big deal though.

Or use a toothpick or old credit card cut to fit in the recess. Neither should be able to scratch the yoyo at all.