WordPress saves media library in the _posts table – you’ll see post_type of attachment for media library items. You’ll notice a guid value in the row, which is the media items default URL.
While unlink()‘ing your file, you can make the file’s full URL. Then use that full URL in a simple database query ($wpdb) stating WHERE guid = '$thefullURL'. That will return the row, and you’ll be able to get the ID of the media library item.
With ID retrieved you can then delete it with WordPress’s wp_delete_post() (which will delete from library and also a bunch of _postmeta jargon)
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