The AIA Project Delivery Knowledge Community (PD) promotes the architect’s leadership role in all project delivery methods by assembling and distributing knowledge and best practices for a variety of project delivery methods, e.g. design-build (DB), integrated project deliveries (IPD), and public-private partnerships (P3).
Unless you had the obligation under your agreement with the Owner to file for the permit, it may be prudent to have the contractor that performed the work go to the city and obtain the permit. Should the Contractor not be a viable option, the Owner should apply for the permit. I often see agency personnel respond "friendlier" and more "helpful" towards homeowners than design professionals.
The first thing to verify is if Bidding Phase and Construction Administration were part of your contract. If they were then you have no choice. If not you should negotiate this as an add service. Once this is understood you can move forward with the submission but I would recommend a meeting with the AHJ to go over the actual project status before making any submission. The contractor that did the work without any permits is ultimately responsible so he/she should attend along with the client. Hopefully you will be able to negotiate a solution for providing the AHJ what is needed to sign off. You could use pictures of the construction or selective demolition to show what has been installed. Much depends on the credibility of the contractor with the AHJ. You are not responsible for what has happened but you can be instrumental in helping to facilitate a solution.
E. Michael Stanley, AIA