GSTR-1 is an account of details of all outward supplies whereas GSTR 3B is the summary of all transactions declared and payments made. Hence GSTR-1 does not cover GSTR-3B. GSTR 3B return or statement (whatever you may call because of recent judgment) is mandatory for filing refund claim. However, Annual Return is a final opportunity to reconcile and rectify the mistakes committed. If the figures of your Annual Returns match with books of account and GSTR-1, refund claim may not be rejected by the department otherwise litigation is the alternative route. Refund claim cannot be rejected because of procedural or technical lapses, especially, in view of the fact that no revenue loss is involved.De facto, Annual return is a final return except Final Return under Section 45.
So you may file refund claim after filing Annual Return.