Blending pastry cream right after cooking: does it change final consistency?
Yes. Yes it does. Unfortunately, I did something similar once, and it basically gave my pastry cream the consistency of creme anglaise. It made a delicious ice cream base, but failed as a cream puff filling.
My best explanation is that the blender destroyed the protein structure of the partially cooked egg, but my attempts to look into it in the past haven't been successful. However I also know that an immersion blender cannot be used to whip egg whites, and in fact makes it much harder to do so. (They did whip somewhat, but still had a kind of slimy texture.)
Having said that, it's hard to comment on your recipe ratios when they aren't included, but the use of a blender definitely changes the texture of cooked custard/pastry cream and makes it much thinner.
If something like this happens again, keep a pan of warm water in reserve. Chocolate will melt at far lower temperatures than would damage your cream. Just place the bowl of cream and stubborn chocolate back over the low heat and stir until melted.