I'm in the process of changing the barrel on a factory upper I have. Got at the rail and muzzle brake off and now it comes to the gas block and I see the set screws have been staked. What is the best way to removed these screws?

A cold chisel  will probably move enough metal to free them up if needed.  Honestly, you'll probably be able to overcome the staking job just by backing the screws out with a hex key.  
Unless there's been some serious deformation of the screw heads, they should be able to push the edges back as they twist out.  

Most staking simply keeps a screw or bolt from loosening due to vibration, rather than being able to resist a mechanical force.

The set screws are too deformed to get a hex key in there, I had a spare gas block I just put on the new barrel. I think I'll just leave it on the barrel for the next owner since it will be in the EE soon, the gas block still has plenty of life left in it.

Dremel enough off to get a hex key in to loosen?

As he pointed out the staking was done too aggressively. The heads were crushed enough that a hex key will no longer enter the head.

If you have a good selection of allen wrenches (preferably including metric), try a wrong size allen wrench.  

Use whatever size will fit between the staking.

It might slip but it will start pushing the deformed metal back into shape. (sometimes this is enough)

Next take the correct allen wrench and grind three consecutive sides tapering down a bit until you can barely start it in the hole.

Then tap the allen wrench with a hammer driving the wrench in and swaging the sides of the sides of the hole until it fits.

Of course you have to have a spare allen wrench of the correct size to sacrifice.

The opposite of this procedure also works if you ever have a rounded out allen head screw.

Strike the socket (hole) squarely with a flat faced hammer.  This usually mashes any displaced metal back into the hole enough to

grab the allen wrench tip enough for removal.  If it isn't enough try using a ball peen hammer to mash the hole.

MBP:  I suppose you could remove the gas tube from the block, but either way something has to give or you likely won't be able to unscrew the barrel nut.  With some care and judicious use of a cold chisel, you can eventually remove those pesky screws.  

The moral of this story is don't stake parts like castle nuts and gas block screws that are likely to need removal during the firearm's service life.  A drop of blue threadlocker on each gas block screw will do the job nicely.  You would think the heat would degrade the threadlocker, and it does a little bit, but not enough to keep it from holding the screws tight.  Same goes for castle nuts on carbine receiver extensions. - CW

Already removed the gas tube and took the barrel out of the upper. This was taken off a factory upper, not sure why they decided to stake the screws, the next owner of the barrel can reuse the gas block and USGI barrel nut or try to remove those screws themselves.