Personally, I would never completely bypass the processing even if you are bringing in a processed source during this time as you could never be sure that there are no overshoots or that the audio is being sent to the transmitter at the right level.
Assuming that your BBP computer is connected to your transmitter, instead of bypassing, select the 6dB Protection Clip preset. This basically removes processing but sets the audio to an appropriate level and passes it through the final clippers which still gives you the final layer of overshoot protection, which is one of the most beneficial features of BBP.