If you run the VAT return again for the month you have submitted, do you get the same VAT return value?

If so run it and manually set the submitted flag. If it creates a different answer, and restoring back to the correct back up is not an option. I would make a manual adjustment,  redo the month, already submitted and then reverse the manual adjustment and do this month.

And make a note never to mess around with restoring to a point before the previous VAT return!

Thanks Ken,

We had to do a manual adjustment in the end, as the VAT return had to be filed today!

There's definitely no way we'll let this happen again!