Looking at the JR East website, it states that if the reserved seat ticket is not picked up by 9pm, it will be cancel automatically. Regarding your seat reserved through the JR-East website,
it seems you can pick up the ticket later in the night.
(I think there was no exception to this deadline;
maybe the rule got modified recently.)
Arrival Day (after 11pm): Pick up JR pass and Shinkansen ticket at Haneda Airport ticket machine Unfortunately,
the JR-East office (in HND Terminal 3) are closed
during the late night and early morning hours.
https://www.jreast.co.jp/e/customer_support/service_center_haneda.htmlEverything going smoothly,
you can get to Shinagawa by Keikyu
(in about 20 minutes),
walk to the JR pathway,
then find a JR Reserved Seat Ticket Vending Machine.
JR ticket vending machines
beside the North Gate and the Central Gate
of Shinagawa Station
are open from around 5 a.m. until 11:50 p.m. every day.
(1) Follow signs for the Keikyu lines.
(2) Buy a 300-yen Keikyu ticket.
(3) Enter Keikyu through the gate.
(4) Ask a Keikyu attendant
which train goes to Shinagawa.
(5) Take a Keikyu train to Shinagawa.
(6) Follow signs for the Takanawa Gate.
(7) Exit Keikyu through the Takanawa Gate.
(8) Turn right,
then go up the escalator or the staircase
to the JR pathway.
(9) Find a JR Reserved Seat Ticket Vending Machine.
https://image.itmedia.co.jp/news/articles/2302/22/l_my_0222jre04.jpghttps://www.jreast.co.jp/mv-guide/img/kenbaiki_img.jpgAlternatively, you can visit a JR ticket booth
near the Yaesu North Gate of Tokyo Station or
near the Iriya Gate of Ueno Station.
- JR-East Train Reservation: User Guide
https://www.eki-net.com/top/tr/guide/receive/index.html#headerM2_01From User Guide:
"
If a pass / ticket is not picked up or usedPassIf you do not pick up or use your pass by 23:30 on the last day of the usage period, you will not receive a refund.
* If you have reserved seats, no refund will be issued after the train departs.
Reserved seat tickets (used with a pass) reserved on this siteIf you no longer require your seat, no fee will be charged, but please make sure to cancel the seat reservation from the website.
If you have reserved seats, pass refunds cannot be issued after the train departs.
Reserved seat tickets (used with a pass) that weren't reserved on this siteIf you do not pick up your ticket by 21:00 on the day before your boarding date, the reservation will be canceled automatically (free of charge)."