@John Use a private web browser. They probably won't appear at all. I think Mastodon checks whenever you click on a notification, to see if it exists and to expand the thread. That's why deleted replies still appear in notifications. They're still in the browser's storage, but when you click on them, the React code does an API call and then removes it since it no longer exists.
You should be able to see the calls if you open the dev tools.
@djsumdog Thanks! I did have an issue with migrating to the master branch on accident (different instance) and saw notification issues that @Gargron pointed out was due to a missing column (maybe this read column now in 3.2.1).