Anyone know what will happen if I try to bake flourless chocolate cake cupcakes with a healthy dollop of whipped cream inside??

I have a similar recipe for cupcakes that uses a mix of cream cheese, eggs and chocolate chips for the creamy center, with a quick "chocolate whacky-cake" batter. You fill the cupcake tins, then put in a spoonful of the cream cheese mixture before baking. Delicious.

Kinda sorta relevantly, there was a cake I made a few times years ago that used whipped cream as leavening; best I remember, it was folded into the batter, which presumably had enough structure to hold up once it started cooking.

Or add a frozen chocolate truffle as a filling , won't be too runny when baked

You should add the cream after the cake comes from the oven. If you want to bake in a filling, try mascarpone instead of whipped cream. That still may run a bit, but it has a chance of holding its shape some.

You'll get a mess- the cream won't hold up to heat. Generally filled cakes and pastries are filled after baking.