I was wondering the same thing whilst watching the movie.
I have a theory; maybe he had another tracking device on him and gave the tracker to Magdalene Shaw in an emergency, private meeting in Cuba. He might've been able to communicate with her somehow by pressing a button or something on the tracking device that may have signaled her to meet him (knowing his exact location she meets him at the restaurant/bar), or maybe he somehow relays his coordinates of where he was going to head to her.
(or) The tracking device could've also been in his car and pressing the red button(the one he uses to make it look like his vehicle needed repair) may have also signaled the van driver to block the camera angle and to Magdalene Shaw that he was going to meet with her there, at that time- he gives her the tracking device to give to one of his team mates- as he finds out during that meeting that Cipher had put the Shaw family through hell, he knew that they want revenge and must've known that Deckard would be up for it. Therefore his master plan had fallen into place.