This is a fairly common issue and likely why states stopped using the engine number as the VIN after '55.
Not all states.
In the mid 60's California was still using engine numbers, and required filing an engine change certificate within 10 days after the swap. When I was building my Model A pickup, I filled out the paperwork truthfully as to the date I put the engine in, and they were going to charge me a fine because it was over 10 days prior, even though there was no current registration. They even wanted a "certificate of non-operation" for the years that it wasn't registered, which required statements from neighbors that it hadn't been driven on the street. They insisted that I was not in compliance even though the truck hadn't been operational till way past the date the engine went in. What a PITA. I went away and filled out a new engine change certificate, fudging the date a bit, and got it licensed. Not sure but California has lightened up a bit, although I haven't tried doing the same thing there since that one time.
