Thanks to everyone for the helpful information.  I will see if I can do a better job of documenting the serial port information.  I may try to if I can get details at the hardware level that I can use to identify what hardware addresses are connected to each COMM port before and after an update.  Maybe that can be used to ease the remapping.

Also, thanks for the confidence in USB to RS232  adapters.  The device I had the problem with was the USB port on the Green Heron RT11 Rotor controller.  I even installed large chunks of ferrite on the cable without success. I may try using an actual USB to RS232 adapter on the Green Heron serial port to see if that works OK within some RF.  

Thanks again for all the good advice,
--
Fred, KC9QQ