You are absolutely right, we definitely cannot ask existing clients to delete pass and register pass again.
1. 10.2.1 beta 1 (passes have not been deleted from Apple Wallet)
Wakes up the phone without any notification (just wakes up the phone) but banner with notification text is displayed when using the phone.
However nothing at all is displayed in notification center.
2. 10.2.1 beta 1 (passes have been deleted from Apple Wallet)
Behavior described by andreiafin Dec 15, 2016 1:57 AM
3. 10.1 (passes have not been deleted from Apple Wallet)
Wakes up the phone and get notification consistently ONLY when user clean the notifcation center before receiving the alert.
As a note: 10.2.1 beta 1 release note is here: http://adcdownload.apple.com/Documentation/Beta_Release_Notes_Dec_14_2016/iOS_10.2.1_beta_Release_Notes.pdf
It does not refer to push notification bug at all unfortunately.