How many invoices and what sort of value are they? Also when you say too early are you talking before the end of the period of the return?
What I'm thinking is if you print off the return you have just done, enter the invoices you need to enter, run the vat return again and it should pick up just the unreconciled ones, then sort of add the figures all up and put them on your return. Without thinking to far into it there shouldn't be a problem with this.
-- Edited by Rhianrach on Wednesday 13th of February 2013 06:50:49 PM
Thanks Steve, I think there will prob be about £3k more vat to reclaim rather than pay over, I think I might submit it manually this time rather than electronically, it's better in my bank than in theirs!