see:
http://clark-technet.com/2010/12/wordpress-self-hosted-plugin-update-api
Basically the idea is to hook your update checking function to the pre_set_site_transient_update_themes filter. The version array key you return from this function will be compared by WP to the current theme version from style.css….
Use the admin_notices action to make your alert message more noticeable
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