You will receive a notification that tells you your quarantine period is over the next morning of your quarantine last date, and MySOS will convert to a normal mode.
If you keep on going in and out of Japan many times, you can use some of the previous information if you agree leaving your registered information and MySOS on your device after finishing quarantine period.
You can convert to “Quarantine Mode” again when you arrive in Japan and read the exclusive QR code.
Regarding how to count the days of your designated quarantine period, we'd like to ask you to refer the HCO website.
The HCO website: https://www.hco.mhlw.go.jp/en/