So the question is when you input the articles are they showing up in the wp_postmeta table (as they should using rssmi_source_link as the key)?
... you can delete your post or whatever, but the url stays in the wp_postmeta table and that is where the plugin checks to see if the article (via the link) has been added at some time (regardless of whether the article has been trashed.
No, it is not as you described! When I delete an unneeded post/title and I empty the trash, the deleted post/title is deleted also (in my case) from the postmeta table. I verified this! The deleted posts have the meta_key '_wp_trash_meta_status', so I can easily identify them. After the empting the trash they disapear from the postmeta table.
A little clarification. My blog is located in a subnetwork of a multisite/multinetwork configuration. The id of blog is '5', so the table has the name 'wpms_5_postmeta'. Maybe your plugin in a multisite/multinetwork configuration works differently as in a common/single install?