Start with the zoning certificate. I too had this happen where there was a question in regards to the zoning of a 2 flat and the certificate was issued as a 3. I would highly recommend you speak with the attorney handling your closing. The certificate is your starting point! If that doesn't solve your problem go to the alderman's office and work with them.
Another issue that may arise, if the above doesn't work & if it is brought to light, is when & was the work done legally meaning with permits. If not, you may still be able to convert however, now you may have to get permits for deconstruction and reconstruction....too many details for this forum.