Invoice not declared in GSTR1

Yes, you can do that. File NIL GST-3B returns. However while filing GST-1 file invoice that has been missed 

yes you can do

The taxpayer will not be protected from the non-filing of Invoices in  GSTR1 although he has filed GSTR 3B.

If the Invoice has been lapsed in GSTR 1 then in the next GST-1 that you file in the upcoming month, these lapsed invoices can be added in that Return.