I don't think they every actually "lost the 200k" wallet, they rather tried to take bitcoin out of their cold storage only too see that the cold storage was (virtually) empty. As far as I can tell they did not have a good way to keep track of their cold storage addresses and they assumed that all were empty. When they later discovered that they controlled 200k in bitcoin they disclosed it.
I suppose it is possible they simply lost 200k BTC, but that's not consistent with their bankruptcy filing. Mt. Gox has always been careful to use the word "disappeared" or the term "unable to access" with regard to the missing bitcoins. To me that implies they knew all along that at least some of the bitcoins were still around, and not, as now claimed, removed by some "massive theft."
They blamed the malleability issue, other exchanges looked into the issue and determined it would really not be a threat to them. There have been reports that malleability could not have done the damage that was done to GOX but the scope of time that this research did was less then the time that GOX was in existence, it would be very possible that a large part of this kind of attack happened several years ago, in GOX's early days when bitcoin was worth much less.This kind of attack could have happened when the price of bitcoin was much lower and would not have had as large of an impact at the time.
From what I can understand, the removal of bitcoins through the exploitation of transaction malleability would require a degree of social engineering. Someone would have to request a refund for bitcoins that appeared to have been sent by Mt. Gox, but supposedly could not be verified by the hacker-recipient. Then a Mt. Gox person would actually have to manually make such a refund. That either suggests that it didn't happen that way, or else if it did, perhaps a confederate of the hacker(s) was operating inside Mt. Gox.
Nevertheless, the scenario as you outline it seems rather far-fetched, because it requires one to believe that Mt. Gox lost track some time ago of how much it had in cold storage. However, there are records of an IRC chat with CEO Mark Karpeles during mid-2011 in which he moves 424,242 BTC from one wallet to another as a demonstration of Mt. Gox's solvency. So, at least by this early date, it appears Karpeles did have a handle on how much was in cold storage.
As far as the bot trading is concerned, anything that says the were manulipating the price of bitcoin is crazy. There is evidence that they were trading on behalf of large investors. If they were buying from others without any "real" person paying the price that the bots paid for the bitcoin and receiving the bitcoin that the bots purchased then the exchange would have a massive shortage of fiat.
True enough, and I can quote you numerous press reports from the fall of 2013, during the big price spike occurring at that time, in which Mt. Gox customers were wanting to withdraw fiat, yet had to suffer very long delays in having their withdrawals completed. That does indeed suggest a shortage of fiat, for otherwise why else would there by these long delays?
If the bots were "trying to suppress he price of bitcoin via a massive uncovered short positiion" then the exchange would have a massive surplus of fiat to the turn of tens (if not hundreds) of millions of dollars. The trades that the bots executed were (almost) always buy orders so a short position would make even less sense. I don't think there is evidence that has been leaked that shows the bots sold bitcoin to that degree.
I'll concede you're right on this point, at least a little, as I've seen no evidence that Markus and Willy (the two bots) ever sold bitcoin--only bought them. Though, that does not change any the basic argument I made. Buying bitcoin without ever paying for them suggests that they were bought on margin. These bitcoins could have been unloaded in a private placement[s). The point being that if the bitcoins, purchased by the bots, were actually never paid for, and afterwards through some means sold, then that effectively constitutes an uncovered short position.
I don't follow your logic to say that GOX would have needed a credit line to fund their short term liquidity needs. It is my understanding that GOX only used one bank (it was in Japan) for receiving deposits from customers and processing withdrawals for customers (and for any other banking needs that the exchange had).
The LOC could be used to handle any situation whenin there was some urgent need to cut a check, or send out a wire transfer, yet Mt. Gox was still awaiting deposits to clear. As previously mentioned, the Swiss investigators, CCI, discovered a pattern of mis-routing deposits bound for Mt. Gox from Europe. These deposits would have been handled by the European network of correspondent banks to Mizuho Bank in Japan.
