It can, please check sofakingtuned.com/FAQ for more info:
Q: DOES THE SFT TUNE DISABLE THE EGR?
With the SFT Stage 2, YES! SFT Stage 2 tune is exclusively off-road use. This will delete your stock exhaust. With either SFT stage 1 or 2 ECU tune, if you select "yes" to "EGR removed?" During...