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I removed my entire egr system. Egr pipe, egr cooler, vac lines, solenoids and butterfly.
The "throttle body" is there so at a determined point programmed into the ecu it will close and allow more exhaust gas to enter the intake manifold. Exhaust Gas Recirculation (EGR). Now the td42 system is very basic and can be removed without anything happening, no engine light, limp mode etc etc. It will not effect boost.
I would recommed, if you havent already, block the egr and remove the butterfly at the very least. Removing the egr cooler will remove some load from your cooling system if you go this far.