Yes, chlorine oxidizes Polyquat 60 though it mostly breaks it up into smaller pieces that are still effective, but eventually it breaks down further and becomes ineffective. So the Buckman Labs (makers of Polyquat) procedure recommends lowering the chlorine level after shocking before adding the Polyquat. It will lessen the amount of Polyquat that is degraded (half the FC level will degrade the Polyquat half as quickly) but should still be enough to get through the winter if the water is very cold.
It is not a disaster if you add the Polyquat at shock levels of chlorine. You'll just see the chlorine level drop more quickly and some of the Polyquat will have been oxidized as a result. It's just less than ideal.