how do i close a shortcut? (its required for cut em off at the path achievment)

I believe Soldiers can plant HE charges and shut down the shortcut.

You need an engineer. I just completed it on Container City(damn I love that map) When a soldier blows up a wall or an Operative hacks a door, you can use an engineer to build it up again

Both of those work. I got it by blowing up a lift in the mission where the Resistance is trying to prevent the Security from getting their agent.