it is inconceivable that it would publish a story this huge that wasn't watertight.'
A bit of a bold statement, no ?
I suspect "watertight" here is journalese. You can't guarantee that every story you publish is correct. Even historians with the benefit of multiple sources and hindsight can't do that. What you can do is check that your story stands up and is watertight. So you use multiple sources and do some checking on them, to make sure they've not got obvious motives to lie - or links between them that suggest a conspiracy. Once you've done all that you go off to the lawyers and make sure that your methods will stand up to getting sued - i.e. you can say you did all possible checking.
Often the lawyers will then send you back to do more homework. With something like this you'll obviously have to satisfy the editor, but also upper management, on the grounds of the financial risk to the company.
After all that, you then approach the people the story is about to see if they're willling to respond. And then do any more checking on what they say. If they deny everything then you have to meet an even higher standard of proof internally, because the legal risk has just shot up massively.
At some point you've then done all you can do - and then have to decide whether to publish or not. If the victims are denying everything, then you either trust your sources and research and risk it - or do nothing. If you do nothing, you may never find out the truth. If you pubilsh, there's a much higher chance the truth will come out. But obviously a much higher risk of getting sued, or being made to look really stupid.