If you want to change your master, then yes you will have to upload a new audio file and that could potentially delay your release date. You should place your order only when your masters are 100% ready
If you want to re-master them with our Instant Mastering tool, then you would have to pay indeed. If however you want to master it yourself (or with the help of a specialized engineer), then you can just upload the mastered file when you place your order