That would be the correct way to disclose it, i.e. on the LE you would put the appraisal in Section B, whereas on the CD, you would put your own internal evaluation in Section A. I guess you could make the argument that the way it worked out was better for the borrower, i.e. he paid less. But, 0% tolerance items are a dangerous game. I would hazard to say that, unfortunately, what you described would require a cure, unless you as the lender do the appraisal yourself, in which case you could say you made a mistake and the appraisal should have been listed in Section A to begin with.
On a separate topic, I hope you met the criteria for doing an internal evaluation. I used to cite violations for that all day as a regulator.