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Don't worry. The lender has already pulled your credit. They will only pull a refresh just before closing. This is done to make sure you haven't opened any lines of credit or increased your payments. Worst case, be prepared to write an good LOE disputing those lates. Explain that you were successful in having them deleted on other two bureaus. Explain that once your loan is closed, you will start a new dispute with that bureau. If you need coaching, call your LO for guidance.
Best wishes to you!