I had 2 techs tell me it was the Nest thermostat. Essentially running them without a C wire, while fully supported by Nest, is not good for any HVAC equipment. The Nest thermostat for my upstairs zone, was doing 2 things. First, it started short cycling the compressor and second it likely caused the compressor to run in reverse.
I was told that both of these issues are due to Nest thermostats power stealing to maintain their battery when not connected via C wire. The power stealing can cause scroll compressors to start running backwards. It interrupts power for a split second. If the scroll is running at the time, the scroll unwinds under pressure and when the power comes back, it continues to run backwards. Also, the power stealing can cause the AC contactor to cycle on and off, which over time causes damages.
There's nothing that I could have done, short of not installing the Nests to prevent what happened. Thankfully, my 1st floor unit did not experience the same issue. When I had the failed system replaced, I had the tech connect the C wire at each air handler and I now run Ecobee thermostats with C wires.