Thank you for your input! On the first point, most of my work has been done cold, however there is a nozzle clean routine that raises the temp to brush the nozzle clean of filament. I will make sure things are stable during further testing, to avoid changes to the toolhead.
When I perused the log, I did see those mentions of the stepper phase change, and was curious about its meaning. Your point that its affecting only two motors is a good one. I will look into this further. I wonder if bad steppers or bad tmc2209 could cause such a thing?