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Now what if you have a tune preloaded all ready... do you set your car back to stock before you do this..I.E putting your stock intake back on and stock tune. Or can you do all this with a tune already loaded !
Do you mean as far as unplugging the battery and resetting the computer? It's completely fine to leave your CAI & tune loaded. I would think that's the best/only way you should do it anyway - having your computer relearn everything with the same setup and tune that's going to be loaded.