I have a slightly different view on this matter. Recently on the GST portal under Services > Returns > Tax liabilities and ITC comparison menu, specific columns (17 to 21) are added for "Payment made, if any through DRC-03". In making payment through DRC-03 also, we now get a dropdown to select "Liability Mismatch - GSTR-1 to GSTR-3B" option. In very near future, after the new Rules are notified for the proposed section 38(2)(b) the portal seem to be considering Financial Year wise checking of liability declared under GSTR-1 vis-a-vis liability paid in GSTR-3B. Any excess payment made through next financial year's GSTR-3B will not be considered (it should, however that is not the point of discussion here) in Tax liabilities and ITC comparison menu which is going to be used pre-dominantly for the purposes of proposed section 38(2)(b). Hence, it is not advisable to declare a particular financial year's liabilities through GSTR-3B of the next financial year. Had it been the case where you had to declare this missed invoice within the same financial year (but different tax period) it would be ideal to declare it in any subsequent tax period's GSTR-3B (within the same financial year). Also consider interest u/s. 50(1) which would apply on gross basis (irrespective of liability to be adjusted with ITC/cash ledger) while declaring these liabilities either through DRC-03 / GSTR-3B.
Hope this helps you in making an informed decision.