Don't walk but run @James Bavaro.
These types of projects come across my desk every other week. I have spoken on these types of projects hundreds of times. I don't know if your Architect is savvy to NYC but if he's willing to charge you $12k to close the permit, then I'd get him to put that in writing guaranteeing that fee and sign it ASAP. The house isn't a legal 2-fam. And if the seller won't budge then you shouldn't be purchasing it as one, but valued as a SFH if they're not willing to complete the leg work for the CO.
The first problem is the permit was opened in 2005 and then built. As others mentioned, you will need to see what inspections, if any, were completed. Often times none were done. Secondly, the DOB clerks NEVER give you the whole picture. They aren't the ones reviewing the forms, plans/drawings to provide the necessary approvals. You will be paying way more than $200 in fees. Mark my words. And lastly, and most problematic, there's been several Building Code changes since 2005. It's likely, especially if no inspections were done, you'll need a full set of documents to show compliance with today's codes. This will trigger a bunch of things that could be costly to change.
Another note about the Architect, if an Architect has to supersede the prior Architect of Record, this brings on a lot of liability since they weren't present for the construction and didn't create any of the documents. $12k is super low in that case.
And as @Mohammed Rahman said, DO NOT proceed with Closing without getting a full grasp of what obtaining the legal 2-fam CO will require and thoroughly discounting the price if you are still willing to purchase. I had a prospective client Close and come to me with a similar situation. I wasn't willing to take on the liability for the cost he wanted. It's been years trying to get it closed out and he has not been successful. I recommended he reach out to the original Architect to see if he'd do it, however with these old projects they may not be practicing architecture any longer or be dead.
DM me to discuss in more detail.
-Jared W. Smith, RA - Principal Architect at Architect Owl PLLC (Licensed in NY & CT)