How do I connect jetpack to an existing blog in wordpress.com

I just migrated a website from Wordpress.com and it was using a custom domain - which is the same domain I am using for the new self-hosted site.

I connected Jetpack using the same Wordpress account that was used for the blog when it was hosted on Wordpress.com but instead of connecting the stats etc. from the migrated blog, it adds the new blog as an additional blog and I lose the history of stats.

Anybody come across this before and know how to resolve?