The midfielder bid farewell to Barcelona today and made his way back to Manchester City.
Flick, ahead of facing Athletic Bilbao, said: "Before Valencia we already considered it. I was aware that he wanted to help us and I know him as a human being and person, but he changed his mind.
"I can only speak well of him."
On talk of Andreas Christensen following Gundogan out the exit door, Flick also said: "Why shouldn't you count on it. I have spoken with him and we have discussed what we see.
"He has had some physical problem and has not trained with us. He is a fantastic player who played a lot last year with some problems. He has to be at 100 percent. At 80 percent he can't help us. We have to help him. It is our priority."