He basically said, "Fix it or other things might break".
That's more or less what I was gonna say too. You broke your EGR tube, and yes it will affect how the truck runs. It will let fresh air into the exhaust and screw with the O2 sensor signals. It will also not allow the engine to get the exhaust gasses that the computer expects it to have during cruising. This can causing pinging, low power, poor running, lower economy, etc.
Fix it if you can find one, but they are getting hard to come by. If you can't find one anywhere, get a block plate for the intake, something to block off the port on the manifold, and a non-egr PCM.