Hope this works out for you. Sounds like the dealer is helping you and not fighting it. I'm glad to hear that.
I have doubts that the crank pulley mod would cause this, but remember you're messing with how the engine was designed. The new pulley could (I mean it's possible, not absolute!) cause internal engine vibrations that might lead to cracking of critical components. Harmonics do play a role in engine longevity.
Best of luck to you!