It difficult to imagine something bad happening as a result of doing something we feel is so good. But here's what is bound to happen, at least a few times...
We need to make sure that our TARGET CFM #'s on the Manual-J reports are representative of the ACTUAL amount of air the system will be moving around the house. This means that the installing contractor may need to modify the CFM targets to match the installed equipment. If you're a rater, and you're working on a Version 3 ENERGY STAR project, be sure you keep these things in mind when you're measuring transfer grille sizes or critiquing a balancing report.
Here's a post I recently did on this topic. Check it out. I would love to hear your thoughts on the topic!