A bit like they did with Eltham Well Hall and Eltham Park in about the mid-1980s, I suppose, although there they also slightly realigned the track.
Another example that no-one has mentioned so far is Putney (National Rail) and East Putney (LU District Line). They could close the existing Putney station and replace it with a new interchange station where the District Line crosses over the Windsor Lines, but that would be less convenient for Putney High Street. For many years there has been talk of creating a second entrance to Putney station off the Upper Richmond Road or Oxford Road, which would make interchange between the two stations more convenient, but so far nothing has ever come of it.