Intrastat vs VAT deadlines

From April this year the intrastat submission deadline moved forward to 21st from 30th of the month.  We always used to prepare intrastat and the quarterly VAT return at the same time to ensure that the figures in Box 9 for arrivals reconciled between VAT and intrastat. It was never a problem to do this at month end, but I now realise that we can't bring forward the VAT return to 21st because the C79 VAT certificate forms don't arrive before this date. So it looks as though we have to leave the VAT accounts open after we report for instrastat and then wait for the C79 form for month 3 to arrive.  Then we have to re-run the VAT reports and carry out a detailed reconciliation of any Box 9 movements since 21st to make sure that VAT and intrastat still match. Am I missing something or is there an easier way to deal with this?