No, in this case the inputs-minus-outputs will still be the original deposit, since those intermediate withdrawals and deposits will cancel out.
Only if you ignore the fee. My bot paid generous amounts in fees over the years, to put it mildly.
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Since MtGOX was not doing what clients thought it was doing, the fee
What if you had two accounts? [...] (If this rule is chosen, I will of course choose not to mention my bot account in my claim.)
I am pretty sure that the court will consider a creditor to be a person (or company), not an account. Creditors will have to identify themselves and state their claims.
If you thought MtGOX was going bankrupt of course you would not have put your money and coins there in the first place.
People with multiple accounts may try to be smart and claim only accounts where they mostly deposited, omitting those from which they mostly withdrew. That would be an attempt to defraud the court (like a contractor claiming a debt that was actually paid in cash), which means jail if caught. For money withdrawals, the risk is too big. For bitcoin withdrawals, the risk may be smaller but an audit with expert assistance may identify the owner of the omitted account.
So far we don't know if MtGox's accounting was bogus or not. Probably not. The leaked data seems to be in good shape. We just know they somehow lost a lot of BTC and some fiat, and we still don't know how this happened. I believe Mark thought he had the BTC until he shut off withdrawals. Madoff knew all along his books were bogus.
The accounting was bogus in the sense that the coins that clients thought they were buyng and selling and/or the money they thought that Mark was keeping for them did not actually exist.
It is risky to state publicly suppositions about crimes, but in restrospect there is only one plausible explanation for the withdrawals delays that started many months before the total block, including why the "malleability bug" was not understood and fixed promptly.
There is another website devoted to the analysis of the database (the one with many colorful plots), whose link I cannot find now. Some of those plots are hard to understand, they seem to show lots of trades at prices well removed from the then-current market prices.
One of the main worries about that database is whether accounts of some "friends" were inflated in order to snatch a large portion of the remaining coins. Also there is the possibility of insider trading, fudging with "dead" accounts, mislabeling of managers' accounts as accounts of friends, etc.. Basically, since the previous management was caught lying (about MtGOX's solvency), and their role in the disappearance of hundreds of millions of dollars has still to be explained, one cannot trust any information that comes from them.