I would call Defra and tell them this situation, and see what they advise. It's a long distance call of course, to the UK, but when I called it was well worth it because I spoke in person to a very helpful woman who put my mind at rest about some questions I had too.
Best to get it from the "horses mouth" as to how to make sure the paperwork can be reconciled. I would guess that a letter from your vet and the initialling of corrections may be adequate but like I say, don't take my word for that, speak to Defra (you can e-mail too but actually speaking in person felt much better to me) and get the real skinny on it.
Hope this helps. It sounds like all is not lost, just these goofs which, while horribly worrying to you and which certainly can't be left uncorrected, I think can be reconciled.