We bought our JR pass and made reservation from/to Tokyo - Shin-Hakodate online with JR East because we will travel during Golden Week.
From Tokyo to Shin-Hakodate, the train will stop at Shin-Aomori. So if we decide get off at Shin-Aomori to visit Hirosaki. Do we have to cancel our leg from Skin-Aomori to Shin-Hakodate before we board the train? It is a courtesy to cancel but our train is at 6:32 am, is the JR ticket office open?
Also, from Shin-Hakodate to Tokyo. Instead of boarding the train at Shin-Hakodate, can we board from Shin-Aomori instead wi.thout changing the reservation
There is no penalty for missing your train, but as a courtesy like you said, it is a good idea to cancel or change your seat reservations to match your plans.
You can do it in any JR office.
But the Tokyo Station office opens at 7:30, so you'd need to do so on the day(s) before, or however you made your seat reservations in the first place, like online.
It's probably OK to miss the train from Shin-Hokadate Hokuto and take your seats from Shin-Aomori - it is unlikely but still possible the train conductors will find you are not on the train and then cancel your whole seat reservation for the entire ride.
All that assumes you would be riding the exact same train as you would from your original seat reservation. Please be aware that for trains like Haybusa there is no unreserved seating - seat reservations are *required*.
If you want to get rid of the worry, then change what you can before your trip, and change anything else when you arrive at Shin-Aomori.