OK I'll try a simpler explanation.
Flybuddy paid his money over in 2005
The last accounts filed at Companies House were to 30/11/2005 no accounts have been filed for the years to 30/11/2006 or to 30/11/2007
Shanley became a Director on 28/2/2007
The amount would not have been on a bank statement, but the company's annual report and accounts should have shown FlyBuddy's advance payment (until FlyBuddy had fully drawn down against it), so yes, Shanley as sole director should have known. The balance sheet would show this quite clearly, as it happens.
Venting your wrath on Shanley won't get you anywhere. Shanley was not there when the money was taken and was not there when the last accounts were drawn up, or even when the next set of accounts were due.
The balance sheet would not show Flybuddy's money. It would have simply reduced the value of current assets. With correct accounting practice Flybuddy's account should have been in credit, which would have served to reduce the balance of accounts receivable, which is part of current assets.
Shanley could be made personally liable if the company continued to trade while it was insolvent. Having liabilities that exceed your assets does not make you insolvent. The company becomes insolvent when it can no longer meet its debts as they become due. This may be due to no fault of the Directors. For example if a major customer goes bust and cannot pay what he owes. On a more spectacular level Northern Rock isn't insolvent because it continues to be able to pay its debts as they become due. If we taxpayers had not stepped when it was unable to obtain finance then it would be. If it had become insolvent it would have been as a result of a change in the lending policies of players in the wholesale money markets who cut off its finance.
Nothing that I've seen in this thread suggests to me that Shanley trousered any funds. It looks more likely to me that he naively took on a failing business that had no proper accounts and subsequently turned out to be a tin of worms. It is normal when someone takes over a business for some cash to change hands. If Shanley paid money for BCT then he's lost it. It's also normal for a bank or other provider of finance to seek personal guarantees from Directors. If he provided those then he will also have lost out.
Flybuddy's best bet is to register his debt with the Official Receiver, who is handling the compulsory liquidation. He almost certainly won't get his money back but he may find out what happened.