Think of a ridiculous example where I am being prosecuted for illegal campaign contributions to Donald Trump. If the prosecution team doctors up some fake checks and bank records listing a billion dollars of contributions and keeps those documents in their own files thats one thing, but if they actually present them to a grand jury or use them in a criminal trial as evidence of my crime, then thats a whole different matter.
I am not a lawyer but I would presume the judge would want to see the actual evidence for why Flynn plead guilty for the sentencing phase. iI the 302 they submitted was doctored, it would seem to me that would be a crime.