If your product is already listed then while converting the listing from Amazon FBM to FBA, kindly select the amazon barcodes to changes the FNSKU of the product.
But When you are creating the listing of your product, choose FBM fulfillment method and then list your product. After listing the product wait for few minutes and then convert your listing to FBA and while converting the listing from Amazon FBM to FBA, kindly select the amazon barcodes to changes the FNSKU of the product. In this way your FNSKU will be changed.