This is a deviation and this deviation has been cleverly covered by the builder by hiding it from the authorities and got OC without mentioning it.
Therefore this OC was obtained fraudulently and now the builder is away whereas you are caught or trapped. You should have objected to the OC at that time itself, or you should have verified the approved plan and objected to the deviation at that time or should have cancelled the booking.
You kept quite all the time just because you wanted the flat somehow, it means you are aware of the said illegality.
If your buyer has any problem due to this, you may have to rectify or look for some other buyer who may not avail bank loan for buying this property.
You can apply for regularisation of the deviation to the authorities with the help of builder and procure fresh OC if possible.