If you get the error: "The same Merchant SKU was found among 3rd Party Listings. Merchant SKU must be unique for each Amazon item.", it means you have such item already presented on Amazon. So M2E Pro prevents it to be listed to avoid problems.
You should perform next steps to solve this problem:
Then already listed item will be moved to M2E Listing and can be synchronized.
Note: If you want to list magento product, which is already on Amazon (same SKU), but use another ASIN, then you should set option Generate SKU in Listing Settings to Yes.