Were there special inspections? If so, did you already submit your final report? If not, then the CO won't be issued.
As for 'voiding your design' - it depends on the jurisdiction. I'd first contact your lawyer to see what, if anything, this might expose you to (I could see a scenario where they might turn around and sue you for damages for delaying the project - but that's a question for your lawyer), then reach out to your state board and the local building official to see what procedures, if any, they have for an EOR removing themselves from a project for reasons of breach of contract. It's one thing to do it because they didn't build what you told them to build, but they're less likely to care about breach of contract.
XR250 - I don't think it was on this year's, but I do remember a question on an insurance renewal application asking for 'bad debts' - the stuff I couldn't collect. Just guessing here, but they might use it as a means of judging the kind of clients you have, and what kind of risks you may be taking as a result. I'd be willing to bet there's a pretty solid correlation between clients that refuse to pay and clients that sue.