Okay I have two corner spots that have been dug at. Luckily my buns are not interested in digging them up anymore so at least the damage hasn't got any worse. I believe this is down to always giving them a toy house to destroy and dig at. This one is the best as it has a cardboard bottom for them dig at:
http://www.cardboardguy.co.uk/
I have also used this one below. This doesn't have a bottom so I put a vet bed underneath it and this stopped them wanting to dig at the carpet.
https://www.thehayexperts.co.uk/Tunnels,+Tents+%2526+Mats.8/Maze+Haven.414.html
If these don't work, or for extra security, use old catalogues and telephone directories. Just pile them on the digging spots and then your bunny will be happily destroying the catalogue instead. You will have to pick lots of bits of cardboard and paper but hey ho thats the joy of being a bunny mommy!