I've checked all 15 route relations and all of these have the same issues as I've previously discussed with you... You do understand that you are breaking things, right?

If you don't believe me, check this tomorrow (the issues shown today are already fixed by me): https://tools.geofabrik.de/osmi/?view=pubtrans_routes&lon=145.08489&lat=-37.82686&zoom=12&baselayer=Geofabrik%20Standard&opacity=0.50&overlays=ptv2_routes_invalid%2Cptv2_error_ways%2Cptv2_error_nodes (it'll show most of these as having errors as you added the ptv2 tag to the routes...)