I felt terrible for him. We informed him that we had to start from scratch and redesign the architecture of the website. We were able to keep the look and, feel of the website. However, it took two months to redesign the site based on proper web information architecture.
The mistake cost my client extra time and money. He had already paid for the website which was never going to rank in the heart of DC in a very competitive industry. If he came to us early in the process, we could have worked with the designer developing the site. We could have shown him the errors he was creating in building the website and saved the client money and time. It took about two weeks to inform the client about the importance of website architecture and the relationship to ranking and client acquisition.