Well unless the EU orders the government to pay it back.
Inland Revenue faces paying out tens of billions in tax refunds
http://www.ft.com/cms/s/0/4c3fcd5a-4287-11e5-9abe-5b335da3a90e.html#axzz4AF0MhB6W
Oh dear once again placing blame at the door of the EU when it should lie much closer to home.
This (I think - its behind the paywall) is about how interest is paid when there has been either overpaid or underpaid tax. Various companies have taken HMRC to court on this on the basis that they believe it should be based on compound interest not simple interest. This is working its way through the UK courts.
It has been heard in the UK High Court - the government lost (nothing to do with the EU).
So the government took it to the UK Court of Appeal - the government lost (again nothing to do with the EU)
The government are seeking to take this to the UK Supreme Court - they might win, but if they don't while we remain in the EU there is a final stage, the European Court of Justice which could bail us out (and would likely do so - see below). If we had left the EU and the Supreme Court ruled against then that would be that, no-where else to go.
But back to the European Court of Justice - actually back in 2012 they ruled that there is no EU law right to compound interest and they kicked it to the UK to sort out.
So in fact it is the UK courts which are ruling in favour of Littlewoods and others getting compound interest and costing the HMRC billions, while the EU have already ruled that they have no right to compound interest.
But then when did a Brexiter ever actually bother with the facts rather than their prejudice that every problem is due to the EU.