Like many others, I've done it for a room or two, with no problems.
You have to do it with some common sense though. Closing off a
register forces the air to now flow through less openings. If you
close off enough, air flow becomes too restricted, which is what sounds
like happened in your previous experience.

If it's never to be done, then why do they install registers all over
the place that can be controlled and shut?