I tested the GTFS-R alerts file and find route_ids match the Sydney Buses GTFS file that was replaced by the Sydney area GTFS file at Transport for NSW. Of course, both are now replaced by the static direct download file here.
This appears to mean that the identifiers in the GTFS-R Alerts match only a non-existent GTFS file.
Is there some way to get GTFS-R Alerts synched with some known GTFS file?