VAT Return on Flat Rate Scheme - Invoice without VAT and VAT-only invoice

I issued two invoices to a single client without VAT while I was waiting for my VAT registration to come through. The effective date for my VAT registration was before the two invoices without VAT were issued. I also registered for the Flat Rate Scheme with the same effective date. Following advice from my accountant, I then issued a VAT-only invoice for the VAT on the first two invoices.

On my VAT Return page, the VAT Payable for the first two invoices (without VAT) is zero, and the VAT Payable for the third (VAT-only) invoice is calculated by multiplying the Value Inc VAT (which in this case is *only* VAT) by the Flat Rate. This has the overall result that the total VAT Payable is much lower than I believe it should be. Here are the figures to illustrate what I mean :-

Invoice 001: £8,500.00 (no VAT)
Invoice 002: £8,075.00 (no VAT)
Invoice 003: £2,486.25 (VAT only)
Total incl VAT: £19,061.25

VAT Payable on invoices 001, 002 & 003: £19,061.25 X 10.5% = £2,001.43

But FreeAgent calculates it as £2,486.25 X 10.5% = £261.06

I now know that what I should have done when my VAT registration came through is to issue credit notes for the first two invoices and then issue new invoices including the VAT. However, since I have already issued (and been payed for) the VAT-only invoice, things seem to be a lot more complicated.

In FreeAgent, I've tried adding credit notes for all 3 issued invoices, and then adding two new invoices including the relevant VAT amounts, but this doesn't seem to reconcile the numbers in the VAT Return page :-

Description     , VAT Payable , Value Inc VAT


Invoice 001     ,        0.00 ,      8,500.00


Invoice 002     ,        0.00 ,      8,075.00


Invoice 003     ,      261.06 ,      2,486.25


Credit Note 005 ,     -892.50 ,     -8,500.00


Credit Note 006 ,     -847.88 ,     -8,075.00


Invoice 007     ,     -261.06 ,     -2,486.25


Invoice 008     ,    1,026.38 ,      9,775.00


Invoice 009     ,      975.06 ,      9,286.25


Totals          ,      517.65 ,     21,505.00

* The initial problem seems to be that the VAT Return is calculating the VAT Payable based on the Value Inc VAT for an invoice and when the invoice is VAT-only this results in paying VAT on VAT.
* Invoice 007 (which is actually a credit note for just the VAT) does successfully cancel out the VAT Payable for Invoice 003, but Credit Notes 005 & 006 generate non-zero values for VAT Payable which do *not* correspond with the zero values for VAT Payable on Invoice 001 & 002.
* As a minor point, I would have thought that Invoice 007 should be labelled as a Credit Note and not an Invoice. The fact that it's only VAT does not change the fact that it is a negative amount.

I may well be approaching this in completely the wrong way, but any help or advice would be very welcome.

Thanks, James.