Get some more nets, or a dog and or maybe a longnet? By the time you have stomped all over the warren blocking holes with bricks, logs and whatever else you can find, the rabbit will know your well and truely waiting outside and you might be hard pushed to get them to bolt, especially if its a deep warren. Besides, no matter how many nets you lay, you`ll always miss one, and like has been said, thats usually where they bolt from.
I think its very kind of the rabbits to let you know you missed a hole. You dont miss it a second time...