As far as the Routes.ini file is concerned, it really makes no difference. You can simply write the route as one long continuous ATS route. As long as you don't create flight plans that treat it as a continuous route, you're OK.
Where the discontinuity is relevant is if you are using mapper.exe to create route maps. In that case, you need to add the "HIDDEN' parameter to the route, ie:
FIX NARUS
HIDDEN
END
FIX APEBE
END
Doing that will, according to the Adaptation guide, mean "the route segment is not to be shown at all."
I don't use mapper.exe myself, so I don't have personal experience with it.
Good luck.
