Actually, that sort of helps the prosecutions case. The FBI got rid of the 10mm handgun because they found it was to much gun for most of thier agents, and very few LE agencies in the US ever adopted the 10mm, much less kept it around.
Which is why they have the .40 loaded to the same levels as the downloaded 10mm they issued.
No, you can still make the case the the FBI spent millions and decided it was the right round to use.
Note that the FBI also no longer uses the .357 magnum or 9mm so are those rounds therefore invalidated?