Notifications are working, but you need to make sure the entry in question is already back in your "reading" or "already read" list. You will need to either wait for it to be recovered automatically, or re-add it yourself for the notifications to pop up.
Since the entries are being recovered from oldest to newest, they are the least likely to receive an update and give you a notification – so waiting it out until your notifications start coming back might take a while.

Am I the only one who's notifications aren't working since the 25 of January?