Hi Emma,
I am assuming you use Sage? When you go to do the Vat return it states there are xxx items in this period and xxx unreconciled - and then asks do you want to include the unreconciled 'yes' or 'no'? It sounds like the unreconciled items have never been reconciled as there should not be a lot of unreconciled items anyway as this usually arises when the vat return has been done for a particular period then you get late purchase invoices etc which should have been included but now you would have to include them in the next return.
Another thing to check is that a previous return has actually been reconciled - go to 'company' then 'manage vat' and this will list all the vat returns reconciled - you will then be able to see if there are any missing.
Also, if you go to the 'financials' you will be able see which items have not been reconciled - any items with an N in the vat column means they have not been reconciled.
Hope this has been some help to you - bit of a nightmare when something like this happens.
Marilyn
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