Burn Notice has had its problems with the city of Miami. The show leased an abandoned community center and turned it into a sound stage, and all its permanent sets are there. Miami's city commissioners saw a way to squeeze more money out of the show and announced the community center would be razed and a park would take its place. This meant demolishing the show's sound stage and forcing a moving of the sets, etc. elsewhere. This started about five years ago, and each time the commissioners agreed to delay their demolition in exchange for a hefty increase in rent. That happened again this year, with the new rent now supposedly at $80,000 a month for a building that was doing nothing but gathering dust until Burn Notice came along. (That's just an estimate and the real figure may not be that high.)
So Maddie's exit and the burning of the loft may be preparation for a move to a different city. However (and it's a big "however"), Jeffrey Donovan says he thinks this seventh season will be the last. So maybe they're just winding things down and calling it a day. That's a shame for a show that's still drawing as many viewers as The Good Wife.