Layered van-der-Waals 2D magnetic materials are of great interest in fundamental condensed-matter physics research, as well as for potential applications in spintronics and device physics. We present neutron powder diffraction data using new ultra-high-pressure techniques to measure the magnetic structure of Mott-insulating 2D honeycomb antiferromagnet FePS$_3$ at pressures up to 183 kbar and temperatures down to 80 K. These data are complemented by high-pressure magnetometry and reverse Monte Carlo modeling of the spin configurations. As pressure is applied, the previously-measured ambient-pressure magnetic order switches from an antiferromagnetic to a ferromagnetic interplanar interaction, and from 2D-like to 3D-like character. The overall antiferromagnetic structure within the $ab$ planes, ferromagnetic chains antiferromagnetically coupled, is preserved, but the magnetic propagation vector is altered from $(0:1:frac{1}{2})$ to $(0:1:0)$, a halving of the magnetic unit cell size. At higher pressures, coincident with the second structural transition and the insulator-metal transition in this compound, we observe a suppression of this long-range-order and emergence of a form of magnetic short-range order which survives above room temperature. Reverse Monte Carlo fitting suggests this phase to be a short-ranged version of the original ambient pressure structure - with a return to antiferromagnetic interplanar correlations. The persistence of magnetism well into the HP-II metallic state is an observation in seeming contradiction with previous x-ray spectroscopy results which suggest a spin-crossover transition.