TBE, I don't really know the answer to that question. There have been suggestions that both the US and the UK are reluctant to accept Nigerian-registered aircraft in their airspace because of the reputation of Air Nigeria, and would prefer the operation to bed down a while before they change that position.
If that is true, then the A340s would presumably have to remain on the British register and be operated by Virgin Atlantic flight deck and engineering until opinions have changed. However, I have no idea if there is any truth in this and would suggest you take it with a large pinch of salt until anything is announced officially!