He can add a mechanic's lien on your house

if that happens, you will need to settle the amount in closing when you sell the house. Title company won't issue title insurance to the buyer if you don't settle.

I understand your intention. However it's really "illegal" to make claim of $11K but later have the roofing company collect only $8K. In reality there are many people have this sort of arrangement with roofing company and get away with not paying for the deductible.

In your case there might be a communication gap, or maybe you just found a roofing company that wouldn't do such arrangement. You should have done some reference check before hiring the contractor. At this stage, you probably have to pay for it.

Since you are selling the house, you can easily add the >$3K to the asking price.