1. You can file a new LUT for FY 20-21.
2. Yes, you are right that one of the main condition of claiming export benefit is that the payment should be received in convertible foreign exchange. This means that you should have an FIRC in place for all the payments you receive from outside India. You need to speak to transferwise guys to provide you an FIRC transferwise must be using some or the other bank's services for converting these US dollars into INR and that Bank must be able to provide the FIRC to transferwise.
3.if you are exporting services that doesn't mean you will have to file a Nil return. Nil return means when you don't provide any kind of services. if you are exporting then you will have to mention the export services in the respective table of gstr-3b. However there will not be any GST payment.