User blog comment:Weedle McHairybug/So, why did Big Boss react with confusion in regards to Cipher? (Spoilers)/@comment-1672596-20100825204929/@comment-1504072-20100825210249

There is no way they would spend all that money and effort just to erase a PSP game's storyline from canon. It's easier for them just to "forget" it, and keeping it canon means that fans are more likely to play it.