I picked my car up this morning. Everything seems to be normal. I didn't notice any reduction in power or fuel economy.
I'm not sure exactly what they did to the car; it's kind of hard to read the service report. I know for certain they didn't replace my EGR valve since I had already had that replaced with the latest part a few months ago. But I'm not sure if they replaced anything else either. I'll have to check the service report more closely. It does say for certain that they performed a reprogramming, and I noticed some of my presets were reset.
All in all, it seems not much has changed and that's probably a good thing. And on a side note, the 4-cylinder 528i loaner I drove returned 24 mpg on my commute vs my car's 32 mpg. So much for the 4-banger being as efficient as the diesel...