No, because your power meter will correctly measure zero power in those spots. The problem with braking is that you're dissipating power at an unknown rate, and as the mathematical model solves for the elevation differences, it "looks" like you've just encounted a very steep uphill section.

In fact, on each lap of my "halfpipe" runs I intentionally soft-pedal on one of the downhill portions to trigger the PT's "autozero" feature within the runs, just as an extra measure to eek the best accuracy out of my runs as possible