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Yes, if you flash back to the stock map and retain the UEL header, you will throw a CEL. If you are hoping to avoid questions about your modifications (for whatever reason), the best solution is to replace your UEL header with the stock header and flash back to stock map. Otherwise, being upfront and honest about your modifications is likely the best solution. If they note an ECU-related TSB, which you elect to have flashed, I would offer to flash back to stock, making them aware of the resultant CEL.
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