The WP import script rewrites the Blogger template in a format suitable to retrieve all the archived posts. If you visit the blog during import you would see the Archives links with a note "Site is down for maintenance, meanwhile get a better blogware", or something like that. When the import finishes the script must restore the template, which in my case did not happen. Thanks to Google cache I was able to restore it back, though I don't need it anymore.
You are right that the script doesn't alter the posts or comments in anyway, but I was only referring to my template as I had customized it a lot.
Anyways, it was my fault not to keep a backup. Kudos to the team for the splendid tool.
Are you guys planning something similar to import "JRoller.com" blogs?