You should select Yes on Skip E Invoices to exclude e invoice details in the GSTR1 return.
To reconcile GST2A with your purchase entries in BUSY, you need to follow these steps:
Step 1: Go to the Administration menu and select Configuration.
Step 2: Choose Features / Options then GST / VAT.
Step 3: Then, enter your GST portal username in the GST Portal User Name field and save it.
Step 3: Next, open the Transaction menu and select GST Misc Utilities.
Step 4: Choose Download GSTR JSON Data
Step 5: Then select Download GSTR2A and download the file after verify the OTP.
Step 6: Now, under the GST Misc. Utilities select the Reconcile GSTR Data option.
Step 7: Select GSTR2A (Party wise) / ( Vch wise).
Step 8: Enter the period and can match your GST portal data with BUSY data.