If you don't have your furnace manual, you can look it up online. Put a thermometer probe into the vent nearest your furnace(it needs to be open for this test), close the desired vents so you have air going where you want it and watch the temperature difference between the coldest area that your furnace is pulling return air from and the temperature coming out of this supply register. You don't want to be on the ragged edge of what your furnace manual specifies for temperature rise and definitely not over it. If you can stay in the temperature rise range, you should be okay.
Be sure you change your filters often when doing this because you've got a more sensitive system to your filters getting clogged when you are closing vents like this.
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