Yes it was the vat liability some older versions used Vat control when you deleted the refunded filed vat the link to the refund from the bank deposit was also deleted

Filing vat again recreated the refund and in the customer file Hmrc you should find the transaction waiting to be received and if you look at available credit it should equal the original filed return as the deposit to bank has not been deleted.

just tick the discounts & credit button top right of icon bar and it applies the waiting credit to the new filed transaction and its all done.

If you have marked the refund as received between the original delete of the first filed vat and theses instructions you might have to reverse that first, I am not sure where exactly you are as you should not have needed to mark it as received. You normally just receive the refund against the new filed vat transaction.