I downloaded the config.inc.php file, opened it in Notepad, and saw the url for the offending website. Changed it back to mine, and uploaded the config.inc.php file again, having changed the CHMOD settings to 644. Ran sitemap generator, and all was well.
Reason I spotted it in the first place (I had been away on holiday for a couple of weeks) was that the sitemap generator ran incredibly slowly, and talked about scanning far more pages than my website has. When I looked more closely, I didn't recognise the names of the pages it was scanning. Managed to stop it before it had overwritten my existing sitemap! (Lucky it ran so slow!)
OK, I guess I will push on with the upgrade.