This question already has an answer here:
I've come back from vacation, and I have an unknown large number of e-mail alerts piled up. Hitting the x in notification center only cleared some of them - I'm assuming it was the last 5 since that's what I have it configured to show.
It seems the only way I can clear them is by hitting "close" on each individual message, but that is ridiculously tedious and I have no idea how long it's going to take. In notification center, only new mails that come in are being shown and dismissable with the general x button.
I've tried switching off mail alerts, removing mail from notification center completely, closing Mail.app and restarting, and nothing clears the old alerts.
Is there a way?
EDIT: this has been happening since Yosemite at least, and is still happening in El Capitan.