Do inspection and handling fees that are collected after closing affect any of the Loan Calculation values on the Loan Estimate and Closing Disclosure?

Inspection and handling fees that are collected after closing are part of the finance charge and do affect the APR.

Additionally, these fees are also included in the In 5 Years total and Total of Payments total. See the commentary to §1026.4(a)(1)(ii)(A) and comment 7(vii) in Appendix D to §1026 for additional details.