You can use the closing disclosure to reflect a change in circumstance if it is too late to issue a revised LE.
Generally you compare the LE to the CD to determine tolerances. If you have a change of circumstance that allows for re-issuing the LE and resetting tolerance you would use that revised LE (or CD if it is within 4 business days of consummation and the change was, therefore, reflected on the CD) for comparing charges. The CFPB has issued a proposal that would clarify when creditors are permitted to re-issue a CD to reset tolerances (https://www.gpo.gov/fdsys/pkg/FR-2017-08-11/pdf/2017-15763.pdf).