The Library of Congress and the New York Public Library both hold originals from 1789. The LOC purchased its version from a manuscript dealer in 1943, and the New York Public Library acquired its copy somewhat earlier.
Where did they come from? There were 14 copies made and signed by the relevant congressional officials (such as John Adams and the Speaker of the House). The one now in the National Archives was the copy retained by the Federal Government, and one was sent to each state. Some of those copies went missing or were destroyed.
Doesn’t this mean that the copies in the LOC and in the NY Library are two of those missing state versions? Don’t they belong to the states to which they were originally sent? Put another way, aren’t these copies stolen property? Not so, they say. The theory of both institutions is that the clerk in the First Congress made some “extra” copies and that these are what they have.
The trouble is that there is no evidence that any extra copies were made. Indeed, when the Library of Congress bought its version in 1943, it was from a dealer who (like Peter Lorre in The Maltese Falcoln) went with the thought that “No questions will be asked” about its origins. Perhaps there is no way of proving which state each copy came from, but an expert might be able to figure that out.