You can do a new certificate if there are changes and ask council if this is ok.
Why don't you phone the helpline for basix and find out the facts from the source re land size. May save you a packet.
http://somersoft.com/forums/showthread.php?t=83231
Have you read this one?
You can leave the architect out of it if they are being pedantic. ;) All you need is to DIY certificate to your understanding of the guidelines.
Good luck.