For the sake of the conversation, we are talking about Professional Engineers (PE) or degreed engineers who are either working for a PE or for a manufacturer, yes?
Train Engineers generally are not very knowledgeable about heating and maintenance guys who have been given the "Engineer" title by some HR person are an insult to the profession.
I do think that redirecting engineers is an art form. Phone calls and trying to explain it verbally almost never works unless you have a positive relationship, to begin with. Your frustration is difficult to mask and they usually get defensive.
I like to do a very clear markup of the plans explaining the concerns and suggesting alternatives. It is important to keep it 100% factual and positive. Clearly state what you are concerned about and why. On the pipe sizing in this example, you would point out that although the design will work, you are concerned that you will get a callback because of noisy pipes. You could also point out the pipe velocities and your experience with pipe erosion.
I usually give them a phone call heads up before sending the markup, I reinforce that I would like to have them read my comments and then would like to set up a time to discuss. Again say nothing confrontational.
Most of the time, when they are faced with just the facts, in writing, they will sign off on the changes. Nobody likes to accept that they made a mistake, especially engineers. If they are faced with the choice of an easy path to correct the mistake with no blame assigned or potentially be called out with "I told you so" and potentially a bill for the changes, I have found they will usually take the easier path.
If you can manage the conversation so the fix seems like their idea, you get extra points.