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If I understand the way the Hypertech system works (I have one for my '95 as well), when you plug the Hypertech unit under the dash, it puts the tuning program (with any options) into the PCM and takes the stock program and puts it in the handheld unit. I know for a fact that in this state, the unit can't be used to program another car, so my guess is that it wouldn't change if you disconnect the battery. A trip to the Chevy dealer would be a different story...
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