If we are refinancing a loan secured by the customer's primary residence with another loan also secured by the primary residence, and the Closing Disclosure (CD) shows a $89.00 principal reduction rather than cash-back, is a Right of Rescission required?

As long as you are the original creditor on the current loan, no.

If the customer received the $89.00 back as a check, rescission would then be required...right?

Correct.