Although they looked totally inconspicuous at first glance, we knew they are unique and special.
is given. Now, what I though is that "Although they looked totally inconspicuous at first glance," is a subordinate clause and the rest is the main clause. Then I realized that with in the main clause a that is omitted, so that it could read "we knew that they are unique and special." Does this make we knew a matrix clause? Then the two predicator would make sense to me.