We only have 200,000 and that's only because the community have found them. Kobayashi has no idea and does nothing in this point. I'm sure, if people does not have reveal the cause, the 200,000 would have been "disappeared" too.
Where did you get that from? Mark himself claimed that he found the 220'000 BTC in an old-format wallet, after filing for bankruptcy. Whether he had really forgotten about them is an open question, but AFAIK it was him who "found" them and told the court about them. Kobayashi had them transferred to an address that he controls (it says so in the papers given out at the last meeting).
There have been discussions long before Mark admit it:
https://bitcointalk.org/index.php?topic=490723.0http://www.reddit.com/r/Bitcoin/comments/1z37zw/mt_gox_has_at_least_200k_btcOnly one day later Mark published this statement (so funny to read in retrospect):
"As a result of our internal investigation, we found that a large amount
of bitcoins had disappeared. Although the complete extent is not yet known, we found
that approximately 750,000 bitcoins deposited by users and approximately 100,000 bitcoins belonging to us had disappeared.
We believe that there is a high probability that these bitcoins were
stolen as a result of an abuse of this bug and we have asked an expert to look at the
possibility of a criminal complaint and undertake proper procedures."
https://www.mtgox.com/img/pdf/20140228-announcement_eng.pdfAnd at this time
we already knew that Gox still must have the 200,000. People went crazy about Mark. So Mark finally had to admit it as he could not deny it any longer without loosing every part of his credibility. And a few weeks later we had to learn that the complete transaction malleability story was a myth, see:
http://arxiv.org/pdf/1403.6676v1.pdf