Ground Plane for Flying Antennas (literally)
Without knowing what other analysis you have done, I would recommend doing what you suggested and flip the PCB so that the ground/reference plane is "up" and the radiator is "down".

While you will probably get some performance with the ground plane down, that will be because of RF leakage around the edge of your finite ground plane, and maybe from reflections from objects above the antenna.  If the ground plane were infinite, you would get absolutely nothing (or close to it) on the ground plane side of the antenna.

Did you or anyone else simulate the antenna performance using an E&amp;M tool such as CST Microwave or HFSS?  There are other tools out there, but those are the two that we use for antenna element pattern analysis and design.