Cleaning Heat Exchangers
To clean a heat exchanger, first run a scraper the length of the flue tubes, making very sure to run the complete length. Then follow with the brush. Again, it is very important that the brush travels the full length of the tube and that a rim of soot not get left to eventually plug the end of the tube.
A several sources for purchasing flue brushes and scrapers are:
Remember, manufacturer's recommendations are just that. They are recommendations. As soot builds up on the fire tubes, it insulates the heat exchange effect. The heat exchanger becomes less efficient. Additionally it changes the pressure at which the chimney drafts, and in so, how the fire burns. So, cleaning them more often than the owners manual suggests is preferred.