Low Probability of Detection (LPD) communication aims to obscure the very presence of radio frequency (RF) signals, going beyond just hiding the content of the communication. However, the use of Unmanned Aerial Vehicles (UAVs) introduces a challenge, as UAVs can detect RF signals from the ground by hovering over specific areas of interest. With the growing utilization of UAVs in modern surveillance, there is a crucial need for a thorough understanding of their unknown nonlinear dynamic trajectories to effectively implement LPD communication. Unfortunately, this critical information is often not readily available, posing a significant hurdle in LPD communication. To address this issue, we consider a case-study for enabling terrestrial LPD communication in the presence of multiple UAVs that are engaged in surveillance. We introduce a novel framework that combines graph neural networks (GNN) with Koopman theory to predict the trajectories of multiple fixed-wing UAVs over an extended prediction horizon. Using the predicted UAV locations, we enable LPD communication in a terrestrial ad-hoc network by controlling nodes' transmit powers to keep the received power at UAVs' predicted locations minimized. Our extensive simulations validate the efficacy of the proposed framework in accurately predicting the trajectories of multiple UAVs, thereby effectively establishing LPD communication.