They are both correct depending on what you're trying to communicate. For the first instance, discussions the Management had with you, implies that at some point discussions were had, and they stopped. The second option "discussions the Management has had with you" implies that discussions were done in the past but they might still be happening. The discussions are still ongoing, and they are not finished yet. Thus, if you're trying to communicate discussions have completely stopped in the past, then option 1. If the discussions were never quite finished and they are still happening, then option 2.

The first sentence sounds correct. You might also remove the "the" used in "the Management." It makes the sentence sound slightly stilted. If you would like to keep the use of "the" you should change that part of the sentence to: "We refer to the discussions that the management has had with you. . ." This makes the sentence sound slightly more natural.

perhaps 1 is right