If u have not paid the tax on the same then first deposit the tax with interest on that (if there is any tax liability) , U can add those bill in ur next gstr1.
But, I don't know what is the penalise about missing sale invoice in GSTR 1 return... If you missed the invoice then show it Your next GSTR 1 return...
I think you are taken the bill value in Your GSTR 3B. If Yes no need to worry about payment...