I was wondering the same thing. Without Atlassian being will to provide an official answer, my guess would also be that the notifications are lost. However that is a terrible model. My account very occasionally claims to exceed the 100 notification per day limit, although it doesn't actually provide any way to verify this claim, track the progress toward reaching the limit or see which Jiras were impacted. The notification log is only for invites and so not helpful, highlighted given that it is blank for all my projects and I'm seeing the notification that the limit is exceeded.
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