Q:

Is it bad to close furnace dampers in order to balance temperatures seasonally?

I have a two story home. As such, it's always hotter on the second floor than the first floor.
As advised by many articles and how-to videos out there, I usually close the dampers in the ducts leading to the first floor in the summer, so that the cold air from the air conditioner is forced to the upstairs vents and then sinks down to the lower level, and vice versa in the winter so the warm air rises.
I'm trying to get a straight answer on whether this is ok or bad. I've now seen many other articles that suggest you should always leave all dampers and vents open all the time because you could cause damage to your furnace by creating unexpected blockages.
But most of those articles seem to be focused around the idea of closing off airflow to a room in order to save on energy costs. That is not my goal. I'm not closing off any rooms by shutting doors or anything. I just want the air to start in one spot and naturally move up or down in order to maintain an even temperature throughout the house.
So should I be able to adjust those dampers and registers? Or should I be concerned that it will damage my furnace?
FYI, the house was a new build in 2012, with a high efficiency furnace and AC unit.
UPDATE:
Even with the air filter out, it was still shutting off. Had a friend in the HVAC industry take a look. I wasn't there at the time, but according to my wife, he suggested that the furnace is too big for my house and that my duct work is smaller than it should be. So it was having trouble carrying the heated air away from the burners fast enough (which
She said that he turned down the gas valve a bit and increased the air flow (not sure how). Been a couple days and it hasn't shut off yet.

A:

Yes, if you close too many dampers, you can overly restrict air flow which will burn out your furnace motor. However, what’s more likely is air flow will increase in the ducts/grills that have not been restricted. When this happens it could create a “whistling” noise because the ducts are too small for the amount of air being pushed down the duct. 
When we design heating/cooling systems, we try to balance the air flow so more air can go where there is greatest heat loss/gain. Partially closing one damper will cause more air to flow to other ducts/grilles. So, yes, you can adjust your houses temperature in various rooms by changing (opening/closing) dampers. 

A:

Too long for a comment.
I agree that closing too many it can cause problems. When installing main trunks in multi story homes I like 60/40 in the main trunks in summer 60% upstairs for cooling and 40% downstairs. In winter 60% down and 40% up. Having these 2 simple marks on 2 dampers makes the seasonal adjustment quick and easy.  By adjusting the main trunks each room on the level stays at the correct flow rate because the individual rooms were not messed with. The problem I have seen with closing down too many vents has been on electric furnaces more than gas in my experience but damage to both is caused by blocking the flow.
What happens with low flow, the elements over heat and trip the safety then they cool and the cycle starts over. This shortens the life of the elements and can cause the thermal snap switch to fail making it look like the element is bad. But other things happen with low air flow on gas units. Low air flow can cause the heat exchange / fire box to crack.
I have seen flex lines blown off and trunk lines split open when too many vents were closed. So these are the reason closing them too much is a bad idea.
Depending on how the duct work is routed you usually can reduce the air flow significantly but don't fully close them. This is when back pressure can start breaking things. Reduced airflow can also be caused by dirty air filters putting a larger load on the blower as Lee Sam mentioned.
So to recap, unless your system was designed to fully close zones keep each one open at least 10% and don't reduce the total flow below 90% unless you have a variable speed unit that can compensate. This will reduce wear and tear on the entire system.

