Here is what I would do. Get a large piece of cardboard and a roll of duct tape. Close the end of the trunk line at the point of use (the vents) in the areas you don't want to heat. Let the furnace run a few times and see what the air flow in the rest of the house is like.....check all the rooms. Listen for any flow noise and time how long the furnace runs. Do this a couple of times. Then close off the entire trunk line and see how that impacts your system.
I suspect you will see an increase in the outlet velocity of the heated air in the other rooms.....some may be more dramatic than others. Will it be enough to be an issue - I don't know. The thing is your furnace is going to produce the same amount of air at the same rate regardless if you have that trunk line open or not. By blocking it at the vents it still functions to some degree as far as the balance of the air flow thru the house. By closing it off at the source, now all that air has to go thru the remaining system. The same volume thru a smaller area increases the velocity. Sizes of these lines and how they are set up and the like can all play a factor.
Your best bet is a small trial and see how it actually affects the house. It isn't going to hurt the furnace, but you may find a curtain flailing in the new velocity or even a whistle being created somewhere that is not desirable, or even just an over all increase in the sound level of the air coming out of the vents. I understand your wanting to use the heated air as effectively as possible by possibly not heating that one trunk line. More than likely you will be fine, but it's always worth a look for piece of mind.
I am not an HVAC professional - my descriptions above are from my previous work in dust collection systems and how we used to have to balance and size collection lines to get the desired results. It was "sucking" this is "blowing" same concept just in reverse. I had sensors, probes, velocity meters and computer models at my disposal - you won't. I don't see it causing an issue, but a little trial will help you sleep better at night or determine if you need to bring a professional in to help adjust the balance & distribution with your recent changes.