Adam,
I remove old sealant from roof mounted items using a vibrating tool with a scraper blade. There are a number of these on the market but I have, and use, a Fein Multimaster. I have never caused any roof damage when using this tool and it goes through old sealant like a knife through butter. It leaves remarkably little sealant behind, so after scraping the old sealant off I usually just wipe down the area with solvent and then apply fresh sealant. If you are working around wires you have to work a little harder to get all the old off but even then the vibrating scraper has never failed me.
By the way, the Fein Multimaster is available through the BAC Amazon link.