When you upload a file to Media Library, some data (mainly metadata like title, description, and so on) is stored in database.
So if you delete file using unlink, you don’t delete any rows from DB – so the attachment will be still visible in Media Library.
If you want to delete attachment from ML, you should use WP functions. wp_delete_attachment might come in handy.
You can use it like so:
<?php wp_delete_attachment( <ID_OF_YOUR_ATTACHMENT> ); ?>