I am not talking about archived messages. Is there a way to see them after they have been deleted? Is there a special software that could do this?
From Facebook Help Center:
No, you can't retrieve deleted messages or conversations. Deleting a message permanently removes it from your inbox.
Keep in mind that deleting a message or conversation from your inbox won't delete it from your friend's inbox. It isn't possible to delete sent or received messages from a friend's inbox.