If using with the selector switch in the L or R setting I would not be concerned about such a double input, because the BL3500 will only amplify one or the other. However, if as I suspect you are using the switch in the line setting, to be on the safe side I would cut the cables as suggested in your last sentence.  I say this because I am unsure how the line detection 'auto-switch on' works and decides which pin to amplify.  The auto-sense logic could be 'L or R but not both' - or it could be looking at the difference between L and R to switch on.  Just a thought, and perhaps others will know for sure!

Alright, I will disconnect the pins. Thanks!