The scanner won't be going to the National Archives. Documents are printed out from the computers provided by CIA in room 3000 using their laser printers, then taken from the archive after being checked and placed in one of the green security bags. (I've done this several times, including today. It's how I got the Project Truth report and some other goodies.)
The flatbed scanner restriction is for scanning original archive materials only, since the risk of damaging them is genuinely unacceptable. (The flatbed restriction is also a bit inaccurate since there are non-flatbed scanners that are allowed - it's more accurate to say that what's forbidden are scanners with moving parts that can interact with the paper or material.)
--Mike