Update.
After 6 days running just fine on my secondary Vera, I decided to move both thermostats over to my primary Vera. I dis-associated both of the thermostats, and associated them to my primary. For about 2 days they worked fine.
This morning, my upstairs thermostat (closest to Vera) was no longer responsive to Zwave commands. Currently the downstairs thermostat still works. Sometime between 11:00PM last night when I last ran a manual command and this morning, the thermostat failed.
My guess at this point is that either the Trane’s are not happy with being part of a network with other devices and acting as a routing node, or something with a plugin or another device on my primary Vera is causing the issues.
Since the Trane thermostats are my only current problem with my Zwave network . I am leaning towards something with the firmware on them with the rest of the network.