Is it not possible to get those important papers back from your wife's parents?
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You will likely have to explain why you want replacements. Saying that your wife's parents have the original documents is not likely a good enough explanation and does sound suspect.
Whatever the procedure is or might be and the advice that might follow for passport replacement they will not come out of US immigration law. In fact, all you need is to go online and read the instructions. If you need to replace Certificate of Naturalization, it is an immigration law issue and again, all you need to do is read the instructions and follow.
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The most appropriate and safest route would be to replace the Naturalization Certificate even if that costs your money.
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