I've always interpreted the passages quoted in the answer by Wildcard to mean that they found the guy responsible for the security of "The Flower of Forgetfulness" and convinced him (by application of female charms) to steal the real "Flower of Forgetfulness" and put a copy ("we're having a facsimile integrated") in its place. No one in the British government is aware of the swap, and the only person in the museum who does know that there's now a fake in place won't talk.
They didn't physically break in and swipe it, but they certainly don't have permission of the British government and the museum operators. They all believe that "The Flower of Forgetfulness" is still there - and everyone can see it still on display.
This passage shows that the folks at General Services certainly don't have the "Flower" legally:
They showed up the next day, apparently empty handed. ‘Well?’ said Clare, ‘well?’
‘Seal the place up, Jay,’ suggested Francis. ‘Then we’ll talk.’ Clare flipped a switch controlling an interference shield which rendered his office somewhat more private than a coffin. ‘How about it?’ he demanded. ‘Did you get it?’
‘Show it to him, Grace.’
Grace turned her back, fumbled at her clothing for a moment, then turned around and placed it gently on the Chief’s desk.
They've smuggled it in, hidden in Grace's clothing. That's not how you transport priceless antiques that you are legally in posession of.