I wouldn't bounce them to one track. If they are 100% identical (=copies) theres no use to have the double anyway, it does not add anything to the sound.
If they are double tracked (=with minor differences) you might bump into phase problems which you can not adress anymore if the tracks are bounced to one. The same goes in the case you create minor differences by nudging or using distortion or EQ.
ADDED LATER:I have never created purposely a 100% phase cancellation, so I don't know how it's shown on the track. Maybe that's what you are experiencing? That means opposite phases of sound wave cancel eachother causing silence.