what is the best way to take an antenna off a two story roof? without damaging the shingles
Most antennas have a steal tripod base with aluminum antenna parts. You can easily brake the aluminum parts off by hand for the most part, a sawzall can help too. Unbolt the steal brackets from the roof and step out and replace the small parts of damaged shingles. If you don’t want to mess with the shingles you could slide a piece of flashing between the two damaged shingles and caulk in place, making sure the flashing extends well above the damaged area.
The best way would be replace shingles where antenna was mounted. Its fast and better than patching the holes where screws were from the bracket. Usually only 3 shingles are needed. Other thing if you dont want to replace shingles you can just use caulking to patch the holes.
Best to just remove the antenna . Then patch any holes in the wood with some tar. And install new shingles where the old ones got damaged . If you do it right it will only be like three shingles . And you can feel safe that you will have no leaks.