Hi Richard -
Yes, the change is expected to be permanent. Unfortunately, there isn't really a right answer in this situation, as V2 will continue to see updates while V1 will fade into legacy. Settings between both versions are not cross compatible and V2 contains a special translation routine to deal with the settings from V1. The main situation this is intended to work around is for teams that are running multiple versions of NCrunch at one time, which would be impossible unless the versions were using different files.
Cheers,
Remco