Were you speaking to a service advisor? The original flash never caused a transmission issue, so it sounds like this individual is not knowledgeable on the subject.
As far as the procedure, it’s a simple PCM calibration update. It doesn’t take more than a half hour start to finish.
He was the Service Mgr. He said that from what he's heard, the original reflash caused some 'problems', but was updated. Based on this info, he suggested to wait until there was more reflashed to see if any other 'problems' resulted from the update.
From what I had seen on other sites, the biggest complaint from the round 1.0 was transmission related. I haven't seen enough comments for round 2.0 to see any sort of pattern.
He implied the reflash was fairly straightforward, but the diagnostics that follow are fairly involved. He suggested that the truck be left for the day should any problems be encountered that require a redo or troubleshooting vs. ya, we'll have that done for you in 45 mins if you want to grab a coffee type of idea.
I'm not sure if this helps. I don't want to mischaracterize his comments or cautions.