Will the dealership be able to tell that my truck was programmed if i put it back to stock tuning before taking it in. I have a Hypertech III in a 02' LB7.

nope, just restore to stock and all is well

Hell if its coming in for a problem that doesn't deal directly with the engine our dealership don't even give a damn if there's a programmer in it or not.

Some dealers are tuner friendly and some are not. But if you are having fuel related issues or driveability issues, return to stock.

if you take it to dealer, remove programer, dealer may try to check/update ecm. if reflashed programmer will need to be reprogramed by mfgr, save yourself the trouble.

I never had a problem with mine as long as I returned it to stock

Does it matter? Is it still under warranty being that old?