It has happened to many people that USCIS lost the supporting documents, especially when the I-140 was e-filed. So, there is a small chance that USCIS lost your package. However, we do see that USCIS RFE says: "The petitioner appears to be part of a talented team doing research that could be of national interest. The team is just one of many that are working on the same type of research- which indicates USCIS know your qualifications."

In your cover letter, you should address all the prongs for NIW by quoting the relevant laws and addressing each of them separately, which means the following prongs issued in the NYSDOT case:

• it must be shown that the alien seeks employment in an area of substantial intrinsic merit;
• it must be shown that the proposed benefit will be national in scope;
• the petitioner seeking the waiver must persuasively demonstrate that the national interest would be adversely affected if a labor certification were required.

It has to be shown that aliens ability to serve national interest is significantly above than available U.S. worker with same minimal qualifications, and it must be shown that the alien has a past record of contributions to areas of national interest justifying future benefit to national interest. When we go through the rest of your RFE, it seems that you haven't addressed each of the prongs separately and established how you satisfy them.