A negative Power Factor either indicates energy export from a Solar or Wind generation system, or when loads are light perhaps a TV or LED lighting they present negative PF values.
The Shelly 3EM is reporting the correct values and PF ranges from -1 to +1 and can’t be converted into an absolute value, this is why the values are now incorrect.
It is not unusual for PF to swing from a negative to positive value frequently as load types or load distribution varies, it’s all quite normal, but much misunderstood.