Let me break this down to what you are going to have to do. Your HUD will need to show the actual costs to the borrower. The contract means nothing for page 2 and page 3.
When you get to page 3, you will have zero's in all portions of the GFE side and the actual numbers on the HUD side.
The seller will give a credit for the the costs, per the contract and the bank will be paying the customer the total 'tolerance' fees due to it's error. You will basically have 100% tolerance cure as 10% of zero = zero.
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My opinion only. Not legal advice.
Say you'll haunt me - Stone Sour