In case you're using the WordPress SEO by Yoast plugin (same author) each article will have two canonical links, which confuses search engines.
With the 'Wordpress SEO by Yoast' plugin you can also configure the canonical URL.
I've used the following sql statements to migrate all settings. Nothing special, but easy to have.
DELETE FROM wp_postmeta WHERE meta_key='_yoast_wpseo_canonical' UPDATE wp_postmeta set meta_key='_yoast_wpseo_canonical' WHERE meta_key='_canonical'