Can I add a missing invoice to the previous conditional progress in the exceptions box with a notation?

With respect to adding a issing invoice t a previous waiver, it is rarely if ever a good idea to modify a document that has already been filled out, executed, and delivered. However, it is unclear from your question how the math and timeline works out with respect to the payment and labor/materials furnished. It appears that the Dec. conditional waiver and the March unconditional waiver relate to the same work since the amounts are equal, and that certain interest charges were not considered when that amount was paid? 

If the $69,276.00 was paid, it should likely be fine that that amount was noted on the unconditional waiver. Note that a California lien waiver, whether conditional or unconditional contains the following language: "This document waives and releases lien, stop payment notice, and payment bond rights the claimant has for labor and service provided, and equipment and materials delivered, to the customer on this job through the Through Date of this document." In California, interest, attorneys' fees, costs of collection or other additional amounts are not allowed to be included in a lien claim , the mechanics lien amount is limited to the reasonable value of the work provided by the claimant, or the price agreed to by the claimant and the person who contracted for the work (less payments already received). Accordingly, if interest isn't lienable, it shouldn't make a difference whether interest only is not contemplated by a lien wiaver document. 

Additionally, CA lien waivers also note that the waiver has no bearing on contract rights, including "rights based on breach of contract." to the extent that the right to recover interest payment is based on the contract between the parties, and/or arises from a beach of the payment provisions in the contract, the enforcement of a claim to recover those amoutns should not be waived by the lien waiver document.