That’s really interesting - looking at my own files, there are times where the power meter stops responding when I stop at a cafe, and having “-” instead of zero does seem to be throwing it off…
Your problem actually spurred me to action and I sent a help ticket to TrainingPeaks about my particular issue (which in my case was the average power being too low). Their response:
The reason for this is that TrainingPeaks calculates Kj from the actual file data itself but the average power is calculated from the summary data of the device.
When a small portion (can be super small so it doesn’t mess up ride data) of the ride is deleted it forces TrainingPeaks to calculate the average power and Kj for the ride.
i.e. “it’s your bike computer’s fault”. Although it’s possible your issue has a different cause.