I'm pretty sure you won't be able to return to stock with the smarty since you overwrote the ECM. Shouldn't hurt anything if you do.
From what I remember the only time a box tuner causes issues with EFILive is if you return to stock then read that stock file out and try to modify it.
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2006 3500 QCSB SLT LoneStar - G56 - 3.73's - LT315/70R17 - Thunder 330 (62/74/14) - 50hp injectors - EFILive - S&B Intake and Horn - Fluidampr - DPS manifold
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