You can only use one basal thermometer at a time with Natural Cycles, as two thermometers simultaneously may cause variations that are too high and may affect the algorithm negatively.
A basal thermometer is highly accurate, but from one thermometer to another thermometer, there can be small differences in how each one measures. An example of this is if one of your thermometers is showing one temperature, the second can show a +/- 0.1°C difference. As the app is looking for the smallest differences when trying to detect ovulation, having two thermometers can cause false temperature fluctuations, even if both thermometers are from us. This incorrect data can cause too high fluctuations, which will make it difficult for the algorithm to confirm ovulation, and you'll be given more red days.
You should be using the same thermometer at all times, and you should not have a thermometer at home and another at your partner's house or similar. If needed, please keep in mind that you should only change to a new thermometer at the start of your next period, as you should not change thermometers in the middle of a cycle.