To give some technical info here, @gianfranco posted a very nice overview of the audio path of the Mod Duo a while back, it can be found in this thread. This still holds mostly true for the MOD DuoX as well. (I do think we need to make this kinda info more easily findable for new users 
)
As can be seen there, the output peak meters are monitoring the digital output going to the DAC, when this value becomes to big for the DAC (digital clipping) they will become blinking red. I would suggest lowering the output level of the pedalboard with for instance a gain plugin at the end or a limiter as @solobasssteve just suggested.
I hope this solves your issue!