Did you plug in to the same USB port? Yes
Here I can unplug and replug devices at any time, whether FS/P3D is running or not. The assignments stay. They are dictated by the Registry, not by FSUIPC. But then though I've got, for instance, two apparently identical Bodnar boards, Windows and therefore FSUIPC distinguishes them by their Serial numbers, which, unfortunately, many devices don't supply on the USB interface.
Are you sure when you say "FSUIPC did not recognize any of the controllers" that the two Pokeys were not simply swapped? Apart from two Pokeys, what others are there? How did you decide FSUIPC didn't recognize them? I launched P3D, then opened FSUIPC then review the axis and button assignments and neither Pokeys responded. Of course when I look in controls in P3D, both PoKeys were recognized.
Deleting JoyNames won't magically make FSUIPC "recognize" joystick devices! the entries there only tell it how to assign them when it hasrecognised them. so I think you are not describing this properly. I deleted all the information under the section of JoyNames and it worked when I restarted FSUIPC.
What probably happened was that, since the Pokeys devices are probably indistinguishable to FSUIPC, it saw them in a different order and so cross-assigned them. the fix is simply to change the numbers or letters or both over in the JoyNames section.
I"ll keep an eye on these errors.
Tim