It's impossible for ovens to be 100% identical no matter how much they try in manufacturing. As a starting point, set them both at the same conditions. If the product results are different, then make small adjustments to the one that is not making a good product. Depending upon the problem, you might need to raise or lower the temperature or change air flow valve settings, or line speed. Always make notes of what your are doing and the effect of what you are doing. Don't make multiple changes at the same time.
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