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This seems to be a recurring problem with some mortgage lendors, who do not want pending disputes.
They incorrectly require removal of any comments pertaining to disputes, extending that requirment to concluded disputes.
A CRA updates the status and comments when a dispute is resolved. For legal reasons, they must preserve the record of prior disputes, and usually will not totally delete record of a concluded dispute. The best you can do is to get the comments updated to show the dispute was resolved.
If the loan officer is demanding that you obtain deletion of any reference to a prior, concluded dispute, I would speak to someone higher in their management chain and explain that consumers do not have any basis for obtaining deletion of legal information retained by a CRA.
Simply removing the remarks shouldn't have affected your score.
Did something else change on your TransUnion report? How long ago was this?
Have you talked to your loan officer? If the other two scores didn't change and they were all close to the same, your middle score might not have changed. The middle score is usually what they go off of.