Replacing engines is one reason the practice of using engine numbers was stopped I believe. When the engine is gone there is no number on the vehicle matching the title. The data plate typically contained the serial number which is not necessarily the same as the VIN shown on the title. Replacement engines from Chevrolet came with a blank boss for the mechanic to re-stamp the number. When "used" engines are swapped the problem you face raises it's ugly head. Folks who change engines without changing the title to reflect the new number (in engine number states) are creating a problem for future buyers. Having said that every state has a method for resolving the problem. The best thing for you to do is call your licensing authority (DMV or whatever it's called in your state) and find out what process they use. Any well intentioned "I did it this way" you may receive here may not be accurate. Get the info from the horses mouth.

Save a life, adopt a senior shelter pet.
The three main causes of blindness: Cataracts, Politics, Religion.
Name your dog Naked so you can walk Naked in the park.