Does it work in the reverse direction in Kanazawa→Shinjuku?
⇒No, three star alps route ticket is only for Shinjuku→Kanazawa direction.
Thank you for showing us your current itinerary.
Here is our recommended route if you will use three star alps route.
Take the bus early in the morning at Shinjuku→get off at Hirayuonsen→Day trip to Kamikochi by taking the local bus→Go back to Hirayuonsen→Go to Takayama by three star alps route, stay over night→Kanazawa
From Kanazawa→Shinjuku, there are several ways to go.
1. Bus https://japanbusonline.com/en/AreaSearch/3130000/4172014
2. Bullet train
Have a nice trip in Japan!
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