Go talk to your insurance agent. I ran into this about 15 years ago with a couple old trucks I bought. I don't recall all of the specifics, but my insurance agent was able to take care of the whole thing.
The whole purpose of this is in case some guy comes out of the woodwork and produces a title for the vehicle after you've fixed it all up, and tries to take it away from you.
I believe they stamp it on your title; but after so many years you're free and clear.